[gmx-users] (no subject)

[James Starlight]

Dear Gromacs users!


I want to simulate membrane receptor in the Gromos 56 force field in the
vacuu and I have some methodological questions.


1- I need to edit topology of my structure by adding one DOUBLE covalent
bond between desires atoms ( they have been already placed in the desired
adjacent positions by pymol).

I add string in topology.top [bonds]

 2809  2810 2gb_5

Does it enough? What addition modification of the topology file requires
for the addition covalent bond?

Where I could found names of all bonds parametrs such as gb_5 ?
I've found that number for the C=O pair so as I understood this must
correspond to double planar bond.

2- I've received message that my system consist of 2 negative charges. For
water-souluble proteins I just place 2 counter ions in the SOLVENT to
neitralize this charge. What I should do for the vacuu simulation ?


Thanks!

James
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[gmx-users] Simulation of membrane protein in vacuu

[James Starlight]

Dear Gromacs users!


I want to simulate membrane receptor in the Gromos 56 force field in the
vacuu and I have some methodological questions.


1- I need to edit topology of my structure by adding one DOUBLE covalent
bond between desires atoms ( they have been already placed in the desired
adjacent positions by pymol).

I add string in topology.top [bonds]

 2809  2810 2gb_5

Does it enough? What addition modification of the topology file requires
for the addition covalent bond?

Where I could found names of all bonds parametrs such as gb_5 ?
I've found that number for the C=O pair so as I understood this must
correspond to double planar bond.

2- I've received message that my system consist of 2 negative charges. For
water-souluble proteins I just place 2 counter ions in the SOLVENT to
neitralize this charge. What I should do for the vacuu simulation ?


Thanks!

James
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[gmx-users] Force Field for Vacuum simulation

[James Starlight]

Dear Gromacs USers!


I'm looking for good force field for the simulation of the
protein-ligand complex in vacuum.

In accordance to the Justin's tutorial I've found that GROMOS96 43b1
force field might be good choice for that task.

But my version of GROMACS lack for that force field .rtps :(

Could you tell me where I could dwnload this force fields parameters?

Thanks,


James
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Re: [gmx-users] Force Field for Vacuum simulation

[James Starlight]

Hi David!

Thanks for reference I'll study it carefully.


I have some general question about the vacuum simulation

1- I've found that common GROMOS fields are not suitable for the
vacuum simulation because of its implementation for condensed phase .
But In some referencces I've found that people use 53.6 ff for the in
vacuum simulation. In addition Ive done minimisation and equilibration
in that ff in vacuum and my system have not been collapse :) Is there
any wy to adopt this ff for the in vacum ?

2- I have uncommon onject for simulation. It's GFP protein where
chromophore group ( like ligand) is covalent bonded to the backbone of
this protein. As I've understood in Justins tutorial there are no any
covalent bonds between protein and ligand. But how I could make this
bond if I operate with TWO topology files ( one for chromophore and
another for protein itself) ? I've done all steps in accordance to
Justins tutorial but on the minimisation step my chromphore dissuse
out of the protein interior because of absent of backbone group.

Thanks again,

James

2012/1/28, David van der Spoel :
> On 2012-01-29 07:20, James Starlight wrote:
>> Dear Gromacs USers!
>>
>>
>> I'm looking for good force field for the simulation of the
>> protein-ligand complex in vacuum.
>>
>> In accordance to the Justin's tutorial I've found that GROMOS96 43b1
>> force field might be good choice for that task.
>>
>> But my version of GROMACS lack for that force field .rtps :(
>
> Because that ff is not well-documented, the only difference with the
> normal gromos43 force field is that the side chains are neutral.
>
> Please check this paper for a comparison of FF for vacuum simulations:
>
> Erik Marklund, Daniel Larsson, Alexandra Patriksson, David van der Spoel
> & Carl Caleman: Structural stability of electrosprayed proteins:
> temperature and hydration effects Phys. Chem. Chem. Phys. 11 pp.
> 8069-8078 (2009)
>>
>> Could you tell me where I could dwnload this force fields parameters?
>>
>> Thanks,
>>
>>
>> James
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Force Field for Vacuum simulation

[James Starlight]

Hi, Justin.

Yes. The GFP chromophore is a part of backbone. It's formed from Ser Tyr
Gly by cyclisation of the Ser with Gly and subsequent dehydrotation. As the
consequence the mature chromophore has cyclised structure wich named as the
CRO residue in PDB structure.

I've made for this CRO residue topology via PRODG server for GROMOS ff.

Than I've imported that new chromophore.top into the topology.top of my
structure in accordance to your tutorial.

Finally I've merged CRO.gro and protein.gro ( I've cut CRO from the pdb for
creation of the topoogy for my protein via pdb2gmx)

Than I've done minimisation and chromophore have been diffused from my
protein :) It seems that I must add covalent bond between CRO and protein
into the topology. But how I could do it for my multi topology file ?

James

2012/1/29 Justin A. Lemkul 

>
>
> James Starlight wrote:
>
>> Hi David!
>>
>> Thanks for reference I'll study it carefully.
>>
>>
>> I have some general question about the vacuum simulation
>>
>> 1- I've found that common GROMOS fields are not suitable for the
>> vacuum simulation because of its implementation for condensed phase .
>> But In some referencces I've found that people use 53.6 ff for the in
>> vacuum simulation. In addition Ive done minimisation and equilibration
>> in that ff in vacuum and my system have not been collapse :) Is there
>> any wy to adopt this ff for the in vacum ?
>>
>> 2- I have uncommon onject for simulation. It's GFP protein where
>> chromophore group ( like ligand) is covalent bonded to the backbone of
>> this protein. As I've understood in Justins tutorial there are no any
>> covalent bonds between protein and ligand. But how I could make this
>> bond if I operate with TWO topology files ( one for chromophore and
>> another for protein itself) ? I've done all steps in accordance to
>> Justins tutorial but on the minimisation step my chromphore dissuse
>> out of the protein interior because of absent of backbone group.
>>
>>
> The GFP chromophore is part of the backbone of the protein, is it not?
>
> The tutorial I have for a protein-ligand complex should not be taken to
> mean that all non-protein entities are physically separate entities.
>  Plenty of cofactors, chromophores, and the like are covalently attached to
> the protein.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
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Re: [gmx-users] Force Field for Vacuum simulation

[James Starlight]

David, Justin

Thanks again for help!


I have just few questions about in vacum sumulation of membrane proteins.


I want to simulate GPCR receptor wich have big transmembrane ( helix)
domain and some connecting loop regions wich are exposed to the solvent.

As I understood in classical vacum simulation all charges must be redused
to avoid its collapse.

I want to build biphastic system water-vacum-water where loops would be in
water and TM helixes in vacum region.

Something like this I've read in old publications about simulation of
bacteriorhodopsin http://ukpmc.ac.uk/abstract/MED/10412722


1- Could you tell me where I could found possible algorithm about builing
of such water-vacum-water system?

2- Also I'd like to specify what should I do with the charges residues. I'd
like to use AMBER-like or OPLS ff for such simulation As I understood I
must neitralize only charges in TM helices and keep residues in LOOP
intact. Might this aproache be correct?


James

2012/1/29 David van der Spoel 

> On 2012-01-29 17:09, James Starlight wrote:
>
>> Hi, Justin.
>>
>> Yes. The GFP chromophore is a part of backbone. It's formed from Ser Tyr
>> Gly by cyclisation of the Ser with Gly and subsequent dehydrotation. As
>> the consequence the mature chromophore has cyclised structure wich named
>> as the CRO residue in PDB structure.
>>
>> I've made for this CRO residue topology via PRODG server for GROMOS ff.
>>
>> Than I've imported that new chromophore.top into the topology.top of my
>> structure in accordance to your tutorial.
>>
>> Finally I've merged CRO.gro and protein.gro ( I've cut CRO from the pdb
>> for creation of the topoogy for my protein via pdb2gmx)
>>
>> Than I've done minimisation and chromophore have been diffused from my
>> protein :) It seems that I must add covalent bond between CRO and
>> protein into the topology. But how I could do it for my multi topology
>> file ?
>>
>
> You need to add the bonds angles etc. The easiest way would be to make a
> special bond (specbond.dat file). You need an rtp entry for your cro group
> as well. Then pdb2gmx makes the necessary bonds.
>
> Of course you can make all the bonds, angles, diehdrals and pairs manually
> as well, but that is tedious and error prone.
>
>>
>> James
>>
>> 2012/1/29 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>
>>
>>
>>
>>James Starlight wrote:
>>
>>Hi David!
>>
>>Thanks for reference I'll study it carefully.
>>
>>
>>I have some general question about the vacuum simulation
>>
>>1- I've found that common GROMOS fields are not suitable for the
>>vacuum simulation because of its implementation for condensed
>>phase .
>>But In some referencces I've found that people use 53.6 ff for
>>the in
>>vacuum simulation. In addition Ive done minimisation and
>>equilibration
>>in that ff in vacuum and my system have not been collapse :) Is
>>there
>>any wy to adopt this ff for the in vacum ?
>>
>>2- I have uncommon onject for simulation. It's GFP protein where
>>chromophore group ( like ligand) is covalent bonded to the
>>backbone of
>>this protein. As I've understood in Justins tutorial there are
>>no any
>>covalent bonds between protein and ligand. But how I could make
>> this
>>bond if I operate with TWO topology files ( one for chromophore and
>>another for protein itself) ? I've done all steps in accordance to
>>Justins tutorial but on the minimisation step my chromphore dissuse
>>out of the protein interior because of absent of backbone group.
>>
>>
>>The GFP chromophore is part of the backbone of the protein, is it not?
>>
>>The tutorial I have for a protein-ligand complex should not be taken
>>to mean that all non-protein entities are physically separate
>>entities.  Plenty of cofactors, chromophores, and the like are
>>covalently attached to the protein.
>>
>>-Justin
>>
>>--
>>==**__==
>>
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>> http://www.bevanlab.biochem.__**vt.edu/Pages/Per

[gmx-users] Application of external forces during MD run

[James Starlight]

Dear Gromacs Users!

I'm looking for some tutorial for the example of the biased MD driven by
appication of the external forces.

For example I have simple system wich consist of the peptide (small
membrane chanell) in vacum where I study effect of some point mutations on
the tight packing (primarily vdv interactions) in that peptide.

In more detailes I want to investigate stability of the mutated peptide by
introducing of the motion of some functional relevant rotameric swithes. So
I'm looking for possibility to apply of external forces on that rotameric
switches.



James
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Re: [gmx-users] Force Field for Vacuum simulation

[James Starlight]

Peter,

Yes the main reason is the CPU economy for such experiment. My current
experiment consist of investigation of the tight paking forces (primarily
vdv effect) in the membrane receptor by inclusion of some point mutations.


Actyally I think that simple biphastic system ( like in the Justin tutorial
but with vacum layer instead of cyclohexane) is exactly that I need. How I
could make such layers system where water dont move into the middle layer?


James





2012/1/30 Peter C. Lai 

> I am not sure of the actual interpretive value of such a methodology.
> Are you just trying to save computational time by not having to simulate
> an all atom bilayer? The solvent layer is going to contribute to the
> majority of the computation cost in the first place. As an example, the
> bilayer we are using for GPCR work consisting of 238 POPC molecules adds
> 30552 atoms out of a total of 99547 atoms, In any case, people have been
> conducting all-atom simulations of opsins since at least 2005 because
> of the availability of computational resources. See: Lemaitre V., Yeagle,
> P.,
> Watts, A. Biochemistry 2005, 44, 12667-12680 . So it is unlikely that
> any reviewers today will accept an opsin system simulated in anything but.
>
> Perhaps a biphasic implicit solvent model would work better for you (unsure
> if gromacs can support an "exterior" dielectric and an interior
> dielectric).
> There may also be some people using a coarse-grained bilayer with an
> all-atom
> protein, but again, unless you have carefully determined the coupling
> parameters between a MARTINI bilayer and an all-atom protein, there will
> be doubts about the usefulness of such a system.
>
> If you really must do without the bilayer, you might be able to get away
> with using strong i,i+4 distance constraints within your TMs to preserve
> helical stability while the entire protein is solvated.
>
>
> On 2012-01-30 10:50:35AM +0400, James Starlight wrote:
> > David, Justin
> >
> > Thanks again for help!
> >
> >
> > I have just few questions about in vacum sumulation of membrane proteins.
> >
> >
> > I want to simulate GPCR receptor wich have big transmembrane ( helix)
> > domain and some connecting loop regions wich are exposed to the solvent.
> >
> > As I understood in classical vacum simulation all charges must be redused
> > to avoid its collapse.
> >
> > I want to build biphastic system water-vacum-water where loops would be
> in
> > water and TM helixes in vacum region.
> >
> > Something like this I've read in old publications about simulation of
> > bacteriorhodopsin http://ukpmc.ac.uk/abstract/MED/10412722
> >
> >
> > 1- Could you tell me where I could found possible algorithm about builing
> > of such water-vacum-water system?
> >
> > 2- Also I'd like to specify what should I do with the charges residues.
> I'd
> > like to use AMBER-like or OPLS ff for such simulation As I understood I
> > must neitralize only charges in TM helices and keep residues in LOOP
> > intact. Might this aproache be correct?
> >
> >
> > James
> >
> > 2012/1/29 David van der Spoel 
> >
> > > On 2012-01-29 17:09, James Starlight wrote:
> > >
> > >> Hi, Justin.
> > >>
> > >> Yes. The GFP chromophore is a part of backbone. It's formed from Ser
> Tyr
> > >> Gly by cyclisation of the Ser with Gly and subsequent dehydrotation.
> As
> > >> the consequence the mature chromophore has cyclised structure wich
> named
> > >> as the CRO residue in PDB structure.
> > >>
> > >> I've made for this CRO residue topology via PRODG server for GROMOS
> ff.
> > >>
> > >> Than I've imported that new chromophore.top into the topology.top of
> my
> > >> structure in accordance to your tutorial.
> > >>
> > >> Finally I've merged CRO.gro and protein.gro ( I've cut CRO from the
> pdb
> > >> for creation of the topoogy for my protein via pdb2gmx)
> > >>
> > >> Than I've done minimisation and chromophore have been diffused from my
> > >> protein :) It seems that I must add covalent bond between CRO and
> > >> protein into the topology. But how I could do it for my multi topology
> > >> file ?
> > >>
> > >
> > > You need to add the bonds angles etc. The easiest way would be to make
> a
> > > special bond (specbond.dat file). You need an rtp entry for your cro
> group
> > > as well. Then pdb2gmx makes the necessary bonds.
> > >
>

[gmx-users] Charge distribution in the topology file

[James Starlight]

Dear Gromacs Users!


I want to perform in vacuum simulation for the simple peptid parametrised
by Amber 99SB and Gromos 43.1 force fields.


As I understoon the primary foal of in vacum simulation in the turn of all
charges in the residues wich are not exposed to the solvent.


>From topology file ( done by Amber) I've found such example for the Gly
residue as well for charged Glu

; residue 404 GLY rtp GLY  q  0.0
  6365  N404GLY  N   6365-0.4157  14.01   ;
qtot -1.848
  6366  H404GLY  H   6366 0.2719  1.008   ;
qtot -1.576
  6367 CT404GLY CA   6367-0.0252  12.01   ;
qtot -1.601
  6368 H1404GLYHA1   6368 0.0698  1.008   ;
qtot -1.531
  6369 H1404GLYHA2   6369 0.0698  1.008   ;
qtot -1.461
  6370  C404GLY  C   6370 0.5973  12.01   ;
qtot -0.8642
  6371  O404GLY  O   6371-0.5679 16   ;
qtot -1.432

; residue  28 GLU rtp GLU  q -1.0
   354  N 28GLU  N354-0.5163  14.01   ;
qtot -2.516
   355  H 28GLU  H355 0.2936  1.008   ;
qtot -2.223
   356 CT 28GLU CA356 0.0397  12.01   ;
qtot -2.183
   357 H1 28GLU HA357 0.1105  1.008   ;
qtot -2.073
   358 CT 28GLU CB358  0.056  12.01   ;
qtot -2.017
   359 HC 28GLUHB1359-0.0173  1.008   ;
qtot -2.034
   360 HC 28GLUHB2360-0.0173  1.008   ;
qtot -2.051
   361 CT 28GLU CG361 0.0136  12.01   ;
qtot -2.038
   362 HC 28GLUHG1362-0.0425  1.008   ;
qtot -2.08
   363 HC 28GLUHG2363-0.0425  1.008   ;
qtot -2.123
   364  C 28GLU CD364 0.8054  12.01   ;
qtot -1.317
   365 O2 28GLUOE1365-0.8188 16   ;
qtot -2.136
   366 O2 28GLUOE2366-0.8188 16   ;
qtot -2.955
   367  C 28GLU  C367 0.5366  12.01   ;
qtot -2.418
   368  O 28GLU  O368-0.5819 16   ;
qtot -3

My qustions:

1- What is difference between charge value and charge B qtot value ?

2- Must I  turn off absolutely all charges even in the non-polar residues
e.g edit
-0.3662 value  to the 0. for all atoms in Gly for instance. ? What
another edition should I do for the elimination of the charges ?

3- I've found that GROMOS force field is not good choise for the vacum
simulation because of non condensive phase of that system but in some works
authors use this ff for in vacum system. What should I do for the
adaptation of that ff for my system?


Thanks

James
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Re: [gmx-users] Force Field for Vacuum simulation

[James Starlight]

Peter,

firstly- thanks for the so detailed discussion.

The negative aspects of water-vacum-water sandwich system wich you provided
indeed keep me from the modelling of such system.

Indeed I found some information about influence of the specific lipids on
the stability of the protein by the regulation of tight packing contacts. I
think that specific cholesterol binding sites in the receptor are very good
example of such regulation due to heigh regidy of the dual apolar rings of
that lipid.

How do you think is there any way to simulate such membrane packing forces
by introducing of the lipid-like layer ? What are the most appropriate
might be in that case? E.g I've found in the Justin's tutorial cyclohexan
layer as the membrane-like solvent but I suppose that ussage of the smaller
apolar mollecule might be more similar to acyl-like interior.

James

2012/2/2 Peter C. Lai 

> On 2012-02-02 11:57:22AM +0300, James Starlight wrote:
> > Peter,
> >
> > Yes the main reason is the CPU economy for such experiment. My current
> > experiment consist of investigation of the tight paking forces (primarily
> > vdv effect) in the membrane receptor by inclusion of some point
> mutations.
> >
> >
> > Actyally I think that simple biphastic system ( like in the Justin
> tutorial
> > but with vacum layer instead of cyclohexane) is exactly that I need. How
> I
> > could make such layers system where water dont move into the middle
> layer?
> >
> >
> > James
>
> The main issue is that vacuum is not a phase. Vacuum is simply empty space.
> A particle's interaciton with vacuum is null, by definition so a
> "biphasic" system with one of the "phases" being nothing is literally not
> comparable to a true biphasic system. You have to realize this from a
> physical point of view... Moreover, how do you know for certain that the
> hydrophobic interaction between TM and lipid does not contribute to the
> TM bundle packing and the interactions you are trying to study? Remember,
> it has been shown that TMs "may flex to satisfy hydrophobic mismatch".
> (Yeagle, et al Biochim Biophys Acta. 2007 Mar;1768(3):530-7)
>
> Is using united-atom bilayer (Berger lipids, from Justin's KALP-15/DPPC
> tutorial) still computationally unacceptable for you? (Tieleman et al 2006
> J. Phys.: Condens. Matter 18 S1221). I did mention earlier also adding some
> coupling parameters to use a coarse-grained bilayer with all-atom protein
> too.
>
> Anyway, if you are really adamant about not using explicit bilayer,
> I thought about this a little. Maybe try using explicit waters in the non-
> membrane portions of the system, then use implicit solvent (GBSA) with
> the correct dielectric to mimic a hydrophobic phase
> I have no methodology for this approach.
>
> If I were to take your request of "How do I use explicit water but vacuum"
> literally: An all-atom system that preserves the vacuum in the membrane
> region
> of the system would involve making a 2 walls of immobile waters:
> You select a monolayer of waters at each end that you want to act as the
> wall. Rename them to a different residue name in your .gro file. Reorder
> the .gro file so that all the wall-water atoms are in their own contiguous
> section. Copy the .itp you use for the mobile waters to another .itp, edit
> and change the moleculetype to your wall residue name. Add the new .itp
> to your .top. Either use freeze_grps or position restraints on the wall
> oxygens to prevent them from moving. This approach has many many problems
> associated with it, not least that of: "what do you do with the waters
> in the solvent accessible space" and the fact that since there is vaccum
> surrounding the outside of the TM bundle and waters inside the TM bundle,
> your protein may explode from the lateral motion of the waters inside the
> solvent accessible spaces pushing against the TMs...
>
> >
> >
> >
> >
> >
> > 2012/1/30 Peter C. Lai 
> >
> > > I am not sure of the actual interpretive value of such a methodology.
> > > Are you just trying to save computational time by not having to
> simulate
> > > an all atom bilayer? The solvent layer is going to contribute to the
> > > majority of the computation cost in the first place. As an example, the
> > > bilayer we are using for GPCR work consisting of 238 POPC molecules
> adds
> > > 30552 atoms out of a total of 99547 atoms, In any case, people have
> been
> > > conducting all-atom simulations of opsins since at least 2005 because
> > > of the availability of computational resources. See: Lemaitre V.,
> Yeagle,
> > > P.,
> >

Re: [gmx-users] Force Field for Vacuum simulation

[James Starlight]

Peter,

thank you it's very intresting survey. I'll try to investigate it
carefully. I've looking for the same issue for along time it's also would
be good to find more recent review on the same topic.

By the way today I've found that the testing on the receptor stability in
the case of some point mutations might not be good with the unbiassed MD
simulation. Some people told me that for most valid result the biased MD by
the aplication of the external forces must be done.  Finally even if i've
done very 'deadly' mutation (e.g strong perturbation of the tight packing
in the functional-relevant region of the transmembrane segment) this effect
could not been seen even in the relatively long trajectory.

By contract that publication wich you provide the different conditions were
tested for the refirement of the X-ray result in the standart MD.

So is there any compromise between both of the methods of the MD?

James
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Re: [gmx-users] Force Field for Vacuum simulation

[James Starlight]

Peter,

1- Yes I've also found that the umbrella simulation is exactly that I need.
Now I'm studing this tutorial more carefully.


2- In other words my second question was: in what exactly situations ( e.g
some kind of point mutation) the unbiassed MD may be enought to detect
unstability of the system (one of that examples you've already mentioned
with the Lys Arg substitutions in TM region ) and in what cases the biassed
MD (e.g the PMF) may be needed?


James
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[gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

[James Starlight]

Dear Gromacs Users!

I have problems during npt equilibration of my solvent box with the CCl4
solvent (I'm preparing this hydrophobic layer for further
membrane-mimicking system).


As the result I want to obtain density value ~ 1.5 for such box but between
2 and 3  ns ( where the desity was 1.3) of such simulation I've obtain error

One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.

1) What should I do in that case ? Should I use larger cutoofs ( I'm using
0.9 nm with the Gromos 56 parameters ) or extend some box vectors ?

2) Initially I've tried to use membrane mimicking dimensions 8.6   6.5
3.0 but during equilibration my box was shrinked to the 8.0 6.0 2.0

How I could present such shrinking ?


James
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[gmx-users] Steered MD simulation

[James Starlight]

Dear Gromacs Users!

I'm investigating activation of the GPCRs receptor in the membrane
Because of potentialy long time required for the activation of such
receptors I want to perform some sort of steered MD simulation. For example
I I want to change rotameric dihedrals of some important swith residues
during the productiv MD run to simulate destabilisation of some cruisial
interactions wich stabilise innactive conformation of the receptor.

some example of such simulation without required detailes could be found
here
http://pubs.acs.org/doi/abs/10.1021/bi0506019


Could you provide me with the simlest example of methodology of such
dihdral changes during simulation as well as application of some external
forces on the specified objects?

James
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[gmx-users] Extract Gro coordinate from trr trajectory

[James Starlight]

Dear Gromacs Users!


I want to extract Gro coordinate file from the unclompleated MD
simulation.  I have big trr file and I'd like to obtain GRO coordinates
wich correspond to the last simulation step on the current moment.

How I could do it?

James
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Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

[James Starlight]

Justin,


Larger cutoffs would not only make the problem worse (read the error
> message carefully and consider the minimum image convention), but it would
> also potentially break the validity of the force field model.  The vdW
> cutoff for Gromos96 should be 1.4 nm, not 0.9 nm, in any case.


This sounds controversially alitle :)

Today I've tried such simulation with the 1.2 cutoffs and obtain the same
error on the 3rd ns ( density was 1.35 )
>From the error message I've understood that the problem was due to the Z-
box vector wich was decreased up to the 3 nm ( this is smaller rhan 2x 1.2
of R_list cutoff ). So in accordance to that message I understood that
cutof must be > 1.5 in the case of my system didnt it?

By the way  I never seen such large cutoff distance in the Gromos
parameters. IS there any else way to solve my problem ?

James
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Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

[James Starlight]

Justin,

I've built my system in accordance to the first way from your Biphgastic
system tutorial.

I've defined system with slight biger (  on 1 nm in each dimension)
dimensions that I needed and place maximym CCl4 molecules in that box by

genbox -ci ccl4.gro -nmol 900 -box  9.6 7.5 4 -o new_box.gro

So I've supposed that I've defined maximum density for such box. How else I
could specify starting density of my box?

2) I've tried use 1.4 VDV cutoff and crash of my system happened almost
alfter first 0.5 ns of simulation. By the way in the KALP tutorial I've
found Cutoff = 1.2. Why in that case you've used such uncommon values ?

James

2012/2/5 Justin A. Lemkul 

>
>
> James Starlight wrote:
>
>> Justin,
>>
>>
>>Larger cutoffs would not only make the problem worse (read the error
>>message carefully and consider the minimum image convention), but it
>>would also potentially break the validity of the force field model.
>> The vdW cutoff for Gromos96 should be 1.4 nm, not 0.9 nm, in any case.
>>
>>
>> This sounds controversially alitle :)
>>
>> Today I've tried such simulation with the 1.2 cutoffs and obtain the same
>> error on the 3rd ns ( density was 1.35 )
>>
>
> Still wrong.  Set rvdw = 1.4 and rcoulomb = 0.9 for Gromos96.  Don't play
> haphazardly with cutoffs.  Use what the force field dictates unless you can
> demonstrate that what you are doing is superior.  The original value of
> rcoulomb was 0.8 with reaction field, but 0.9 is fine in the case of PME.
>
>
>   From the error message I've understood that the problem was due to the
>> Z- box vector wich was decreased up to the 3 nm ( this is smaller rhan 2x
>> 1.2 of R_list cutoff ). So in accordance to that message I understood that
>> cutof must be > 1.5 in the case of my system didnt it?
>>
>>
> No, absolutely not.  You don't *want* the cutoffs to be equal to twice the
> box vector, they must always be *less* than this amount to avoid spurious
> PBC interactions due to minimum image violations.  Are you familiar with
> this concept and its implications?
>
> http://www.gromacs.org/**Documentation/Terminology/**
> Minimum_Image_Convention<http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention>
>
> You said in your first message:
>
>
> "2) Initially I've tried to use membrane mimicking dimensions 8.6   6.5
> 3.0 but during equilibration my box was shrinked to the 8.0 6.0 2.0"
>
> So your problem comes from the box shrinking to 2.0 nm in the z-dimension,
> which is less than twice your longest cutoff.  Your box is compressing in
> all directions, which means your initial configuration is too diffuse and
> the application of NPT conditions is squishing it together to arrive at the
> density the force field model predicts.  Build a system with an initial
> density closer to the target value.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
> --
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Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

[James Starlight]

Justin,

2012/2/6 Justin A. Lemkul 

>
>  Some simple calculations using the desired density and the box dimensions
> (to get the volume) will tell you exactly how many molecules you need.  If
> you only "suppose" you've got a reasonable number, there are better ways to
> be sure ;)
>
>
In accordance to my calculations I need in ~ 1000 CCl4 to obtain 1.600
g/cm^-3 density with my box dimensins

By the way way I try to define such system by

genbox -ci ccl4.gro -nmol 1000 -box 8.6 6.5 3 -o ccl4_box.gro

I've obtain memory error :(


Is there any other way to define such system with the desired size and
n_mollecules with the less computation demands?


James
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Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

[James Starlight]

Justin,

Firstly I've created the box of desired size with only 500 molecules ( I
need 1000)

Than I've tried to add extra 200 molecules by means of Genbox

genbox -cp super_box.gro -ci Ccl4.gro -nmol 200 -o new_solv.gro

but no molecules have been added
Added 0 molecules (out of 200 requested) of Cl4

also I've tried

genbox -cp super_box.gro -cp Ccl4.gro -nmol 200 -o new_solv.gro

but system were crashed with message

Reading solute configuration
God Rules Over Mankind, Animals, Cosmos and Such
Containing 2500 atoms in 500 residues
Initialising van der waals distances...

WARNING: masses and atomic (Van der Waals) radii will be determined
 based on residue and atom names. These numbers can deviate
 from the correct mass and radius of the atom type.

Reading solvent configuration
"God Rules Over Mankind, Animals, Cosmos and Such"
solvent configuration contains 5 atoms in 1 residues


Is there any ways to add extra mollecules to the pre defined box ?

James
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Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

[James Starlight]

Mark,

I've checked only density value

with 500 molecules Ccl4 I have  density that is twisely less that I need (
in accordance to the literature ). Also I've checked my box visually and
found that the box is not properly tightly packed so I dont know why genbox
didnt add some extra mollecules :(

In other words I wounder to know if  there is any way to add some extra
molecules to the pre defined box to make my system more tighly packed  ( to
short distance between existing molecules and place new ones in the new
space ) ?

James

2012/2/14 Mark Abraham 

> On 14/02/2012 4:57 PM, James Starlight wrote:
>
>> Justin,
>>
>> Firstly I've created the box of desired size with only 500 molecules ( I
>> need 1000)
>>
>> Than I've tried to add extra 200 molecules by means of Genbox
>>
>> genbox -cp super_box.gro -ci Ccl4.gro -nmol 200 -o new_solv.gro
>>
>> but no molecules have been added
>> Added 0 molecules (out of 200 requested) of Cl4
>>
>
> ... then there are no gaps large enough to insert your molecules. Either
> make gaps, or check out genbox -h for advice on defining the radii.
>
>
>
>> also I've tried
>>
>> genbox -cp super_box.gro -cp Ccl4.gro -nmol 200 -o new_solv.gro
>>
>
> Two -cp options is not what you want, and -nmol probably only works with
> -ci.
>
>
>
>> but system were crashed with message
>>
>> Reading solute configuration
>> God Rules Over Mankind, Animals, Cosmos and Such
>> Containing 2500 atoms in 500 residues
>> Initialising van der waals distances...
>>
>> WARNING: masses and atomic (Van der Waals) radii will be determined
>> based on residue and atom names. These numbers can deviate
>> from the correct mass and radius of the atom type.
>>
>> Reading solvent configuration
>> "God Rules Over Mankind, Animals, Cosmos and Such"
>> solvent configuration contains 5 atoms in 1 residues
>>
>>
>> Is there any ways to add extra mollecules to the pre defined box ?
>>
>
> Yes - but there has to be room for them.
>
> Mark
>
> --
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Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

[James Starlight]

It seems that I've fixed that problem by reduce vdv radii for Cl during
defining of my box

Eventually I've obtained box with the desired density
 than I've delete vdvradii.dat for my wor dir

by when I've launched equilibration I've oibtained

Fatal error:
Too many LINCS warnings (1598)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file

I've never seen this before

I'm using 1.o cutoff for pme and 1.4 for vdv
my LINKS parameters are

; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy atom-H bonds)
constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy

How I could solve it?


James

2012/2/14 James Starlight 

> Mark,
>
> I've checked only density value
>
> with 500 molecules Ccl4 I have  density that is twisely less that I need (
> in accordance to the literature ). Also I've checked my box visually and
> found that the box is not properly tightly packed so I dont know why genbox
> didnt add some extra mollecules :(
>
> In other words I wounder to know if  there is any way to add some extra
> molecules to the pre defined box to make my system more tighly packed  ( to
> short distance between existing molecules and place new ones in the new
> space ) ?
>
> James
>
>
> 2012/2/14 Mark Abraham 
>
>> On 14/02/2012 4:57 PM, James Starlight wrote:
>>
>>> Justin,
>>>
>>> Firstly I've created the box of desired size with only 500 molecules ( I
>>> need 1000)
>>>
>>> Than I've tried to add extra 200 molecules by means of Genbox
>>>
>>> genbox -cp super_box.gro -ci Ccl4.gro -nmol 200 -o new_solv.gro
>>>
>>> but no molecules have been added
>>> Added 0 molecules (out of 200 requested) of Cl4
>>>
>>
>> ... then there are no gaps large enough to insert your molecules. Either
>> make gaps, or check out genbox -h for advice on defining the radii.
>>
>>
>>
>>> also I've tried
>>>
>>> genbox -cp super_box.gro -cp Ccl4.gro -nmol 200 -o new_solv.gro
>>>
>>
>> Two -cp options is not what you want, and -nmol probably only works with
>> -ci.
>>
>>
>>
>>> but system were crashed with message
>>>
>>> Reading solute configuration
>>> God Rules Over Mankind, Animals, Cosmos and Such
>>> Containing 2500 atoms in 500 residues
>>> Initialising van der waals distances...
>>>
>>> WARNING: masses and atomic (Van der Waals) radii will be determined
>>> based on residue and atom names. These numbers can deviate
>>> from the correct mass and radius of the atom type.
>>>
>>> Reading solvent configuration
>>> "God Rules Over Mankind, Animals, Cosmos and Such"
>>> solvent configuration contains 5 atoms in 1 residues
>>>
>>>
>>> Is there any ways to add extra mollecules to the pre defined box ?
>>>
>>
>> Yes - but there has to be room for them.
>>
>> Mark
>>
>> --
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>>
>
>
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Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

[James Starlight]

This also was solved by the some extra minimisation steps.


I've forced with another problem :D

During npt equilibration my system have slightly expanded so my desired
volume and density were perturbed.

I've noticed the below options in npt wich could help me

ref_p= 1 1
compressibility = 4.5e-5

 i'm using this compressibility value   because I'm modelling the
lipid-like environment so I think that I must increase pressure.  Could you
remind me the dependence of pressure from density and volume for liquids ?
:)

James



2012/2/14 James Starlight 

> It seems that I've fixed that problem by reduce vdv radii for Cl during
> defining of my box
>
> Eventually I've obtained box with the desired density
>  than I've delete vdvradii.dat for my wor dir
>
> by when I've launched equilibration I've oibtained
>
> Fatal error:
> Too many LINCS warnings (1598)
> If you know what you are doing you can adjust the lincs warning threshold
> in your mdp file
>
> I've never seen this before
>
> I'm using 1.o cutoff for pme and 1.4 for vdv
> my LINKS parameters are
>
> ; Bond parameters
> continuation= no; first dynamics run
> constraint_algorithm = lincs; holonomic constraints
> constraints= all-bonds; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter= 1; accuracy of LINCS
> lincs_order= 4; also related to accuracy
>
> How I could solve it?
>
>
> James
>
>
> 2012/2/14 James Starlight 
>
>> Mark,
>>
>> I've checked only density value
>>
>> with 500 molecules Ccl4 I have  density that is twisely less that I need
>> ( in accordance to the literature ). Also I've checked my box visually and
>> found that the box is not properly tightly packed so I dont know why genbox
>> didnt add some extra mollecules :(
>>
>> In other words I wounder to know if  there is any way to add some extra
>> molecules to the pre defined box to make my system more tighly packed  ( to
>> short distance between existing molecules and place new ones in the new
>> space ) ?
>>
>> James
>>
>>
>> 2012/2/14 Mark Abraham 
>>
>>> On 14/02/2012 4:57 PM, James Starlight wrote:
>>>
>>>> Justin,
>>>>
>>>> Firstly I've created the box of desired size with only 500 molecules (
>>>> I need 1000)
>>>>
>>>> Than I've tried to add extra 200 molecules by means of Genbox
>>>>
>>>> genbox -cp super_box.gro -ci Ccl4.gro -nmol 200 -o new_solv.gro
>>>>
>>>> but no molecules have been added
>>>> Added 0 molecules (out of 200 requested) of Cl4
>>>>
>>>
>>> ... then there are no gaps large enough to insert your molecules. Either
>>> make gaps, or check out genbox -h for advice on defining the radii.
>>>
>>>
>>>
>>>> also I've tried
>>>>
>>>> genbox -cp super_box.gro -cp Ccl4.gro -nmol 200 -o new_solv.gro
>>>>
>>>
>>> Two -cp options is not what you want, and -nmol probably only works with
>>> -ci.
>>>
>>>
>>>
>>>> but system were crashed with message
>>>>
>>>> Reading solute configuration
>>>> God Rules Over Mankind, Animals, Cosmos and Such
>>>> Containing 2500 atoms in 500 residues
>>>> Initialising van der waals distances...
>>>>
>>>> WARNING: masses and atomic (Van der Waals) radii will be determined
>>>> based on residue and atom names. These numbers can deviate
>>>> from the correct mass and radius of the atom type.
>>>>
>>>> Reading solvent configuration
>>>> "God Rules Over Mankind, Animals, Cosmos and Such"
>>>> solvent configuration contains 5 atoms in 1 residues
>>>>
>>>>
>>>> Is there any ways to add extra mollecules to the pre defined box ?
>>>>
>>>
>>> Yes - but there has to be room for them.
>>>
>>> Mark
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
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Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

[James Starlight]

Mark,


due to hight density the volume of my system have been slightly increased
and during NPT phase I've obtained error

Fatal error:
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.

I'm using 0.9 for electrostatic and 1.4 for vdw cutofs and the dimensions
of my box was 6.5 3 3 on the initial step and 6.6 3 3.3 before crush :)

I want prevent such expansion of my system by increasing of pressure and/
or compressibility but I have not found exact sollution yet.


James


2012/2/14 Mark Abraham 

>  On 14/02/2012 11:01 PM, James Starlight wrote:
>
> This also was solved by the some extra minimisation steps.
>
>
> I've forced with another problem :D
>
> During npt equilibration my system have slightly expanded so my desired
> volume and density were perturbed.
>
> I've noticed the below options in npt wich could help me
>
> ref_p= 1 1
> compressibility = 4.5e-5
>
>  i'm using this compressibility value   because I'm modelling the
> lipid-like environment so I think that I must increase pressure.  Could you
> remind me the dependence of pressure from density and volume for liquids ?
> :)
>
>
> Your forcefield, simulation cell contents and .mdp settings will determine
> the equilibrium density. Whether you need to do anything depends on whether
> you've made a statistically significant post-equilibration measurement of
> your average density. Haphazardly increasing the reference pressure for the
> coupling will reduce the volume, but now you are simulating at that
> pressure. See http://www.gromacs.org/Documentation/Terminology/Pressurefor 
> background info.
>
> Mark
>
>
>
> James
>
>
>
> 2012/2/14 James Starlight 
>
>> It seems that I've fixed that problem by reduce vdv radii for Cl during
>> defining of my box
>>
>> Eventually I've obtained box with the desired density
>>  than I've delete vdvradii.dat for my wor dir
>>
>> by when I've launched equilibration I've oibtained
>>
>> Fatal error:
>> Too many LINCS warnings (1598)
>> If you know what you are doing you can adjust the lincs warning threshold
>> in your mdp file
>>
>> I've never seen this before
>>
>> I'm using 1.o cutoff for pme and 1.4 for vdv
>> my LINKS parameters are
>>
>> ; Bond parameters
>> continuation= no; first dynamics run
>> constraint_algorithm = lincs; holonomic constraints
>> constraints= all-bonds; all bonds (even heavy atom-H bonds)
>> constrained
>> lincs_iter= 1; accuracy of LINCS
>> lincs_order= 4; also related to accuracy
>>
>> How I could solve it?
>>
>>
>> James
>>
>>
>> 2012/2/14 James Starlight 
>>
>>> Mark,
>>>
>>> I've checked only density value
>>>
>>> with 500 molecules Ccl4 I have  density that is twisely less that I need
>>> ( in accordance to the literature ). Also I've checked my box visually and
>>> found that the box is not properly tightly packed so I dont know why genbox
>>> didnt add some extra mollecules :(
>>>
>>> In other words I wounder to know if  there is any way to add some extra
>>> molecules to the pre defined box to make my system more tighly packed  ( to
>>> short distance between existing molecules and place new ones in the new
>>> space ) ?
>>>
>>> James
>>>
>>>
>>> 2012/2/14 Mark Abraham 
>>>
>>>> On 14/02/2012 4:57 PM, James Starlight wrote:
>>>>
>>>>> Justin,
>>>>>
>>>>> Firstly I've created the box of desired size with only 500 molecules (
>>>>> I need 1000)
>>>>>
>>>>> Than I've tried to add extra 200 molecules by means of Genbox
>>>>>
>>>>> genbox -cp super_box.gro -ci Ccl4.gro -nmol 200 -o new_solv.gro
>>>>>
>>>>> but no molecules have been added
>>>>> Added 0 molecules (out of 200 requested) of Cl4
>>>>>
>>>>
>>>>  ... then there are no gaps large enough to insert your molecules.
>>>> Either make gaps, or check out genbox -h for advice on defining the radii.
>>>>
>>>>
>>>>
>>>>> also I've tried
>>>>>
>>>>> genbox -cp super_box.gro -cp Ccl4.gro -nmol 200 -o new_solv.gro
>>>>>
>>>>
>>>>  Two -cp options is not what yo

Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

[James Starlight]

Mark,

I've used that dimensions in accordance to some literature where the same
membrane-mimicking simulation were performed.

I've tried to rise cutoffs and dicrease integration step but my system have
been stil crashed during npt.

I'm using
 pcoupl= Parrinello-Rahman

wich I've found in the KALP tutorial because I have not found the same npt
example file in the Biphastic tutorial :)
Could you advise me another p_coup algorithm for my Ccl4 system?

James

-- Forwarded message --
From: Mark Abraham 
Date: 2012/2/15
Subject: Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4
layer
To: Discussion list for GROMACS users 


 On 15/02/2012 4:45 PM, James Starlight wrote:

Mark,


due to hight density the volume of my system have been slightly increased
and during NPT phase I've obtained error

Fatal error:
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.

I'm using 0.9 for electrostatic and 1.4 for vdw cutofs and the dimensions
of my box was 6.5 3 3 on the initial step and 6.6 3 3.3 before crush :)

I want prevent such expansion of my system by increasing of pressure and/
or compressibility but I have not found exact sollution yet.


Your system is dangerously small for those cut-offs if your initial density
is not correct for your model physics. Your y and z dimensions only just
contain a full cut-off sphere. You should also make sure you are following
the advice about choice of P-coupling algorithm in manual 3.4.9, and
consider using a very small integration time step. I remain unconvinced by
this thread that you have generated a starting configuration that does not
have atomic clashes.

Mark




James


2012/2/14 Mark Abraham 

>  On 14/02/2012 11:01 PM, James Starlight wrote:
>
> This also was solved by the some extra minimisation steps.
>
>
> I've forced with another problem :D
>
> During npt equilibration my system have slightly expanded so my desired
> volume and density were perturbed.
>
> I've noticed the below options in npt wich could help me
>
> ref_p= 1 1
> compressibility = 4.5e-5
>
>  i'm using this compressibility value   because I'm modelling the
> lipid-like environment so I think that I must increase pressure.  Could you
> remind me the dependence of pressure from density and volume for liquids ?
> :)
>
>
>  Your forcefield, simulation cell contents and .mdp settings will
> determine the equilibrium density. Whether you need to do anything depends
> on whether you've made a statistically significant post-equilibration
> measurement of your average density. Haphazardly increasing the reference
> pressure for the coupling will reduce the volume, but now you are
> simulating at that pressure. See
> http://www.gromacs.org/Documentation/Terminology/Pressure for background
> info.
>
> Mark
>
>
>
> James
>
>
>
> 2012/2/14 James Starlight 
>
>> It seems that I've fixed that problem by reduce vdv radii for Cl during
>> defining of my box
>>
>> Eventually I've obtained box with the desired density
>>  than I've delete vdvradii.dat for my wor dir
>>
>> by when I've launched equilibration I've oibtained
>>
>> Fatal error:
>> Too many LINCS warnings (1598)
>> If you know what you are doing you can adjust the lincs warning threshold
>> in your mdp file
>>
>> I've never seen this before
>>
>> I'm using 1.o cutoff for pme and 1.4 for vdv
>> my LINKS parameters are
>>
>> ; Bond parameters
>> continuation= no; first dynamics run
>> constraint_algorithm = lincs; holonomic constraints
>> constraints= all-bonds; all bonds (even heavy atom-H bonds)
>> constrained
>> lincs_iter= 1; accuracy of LINCS
>> lincs_order= 4; also related to accuracy
>>
>> How I could solve it?
>>
>>
>> James
>>
>>
>> 2012/2/14 James Starlight 
>>
>>> Mark,
>>>
>>> I've checked only density value
>>>
>>> with 500 molecules Ccl4 I have  density that is twisely less that I need
>>> ( in accordance to the literature ). Also I've checked my box visually and
>>> found that the box is not properly tightly packed so I dont know why genbox
>>> didnt add some extra mollecules :(
>>>
>>> In other words I wounder to know if  there is any way to add some extra
>>> molecules to the pre defined box to make my system more tighly packed  ( to
>>> short distance between existing molecules and place new ones in the new
>>> space ) ?
>&

[gmx-users] Placing ions in the specified positions

[James Starlight]

Dear Gromacs users!


I've constructed my biphastic system with the water-ccl4-water layers where
in the ccl4 layer I've placed my membrane protein.

Now I'd like to place addition 5 Cl ions to the bottow leafleat of water to
mimick the 'positive-inside rule' (my protein consist of 5 Lys) of the
membrane protein topology. How I could specify to place some ions in the
desired possitions? As i understood the genion place ions in the random
possitions so I've obtained 3 ions in the bottom and 2 in the upper layer.

Thanks

James
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Re: Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

[James Starlight]

Mark,

I'm using exact all parameters wich I found in different experimental work.

By the way reducing of integration step to 1fs provide me with better
equilibration of the Ccl4 system  ( I've being obtained stabile system
during 3 ns)

but I had a problems during ntp equilibration when I inserted test peptide
into that pre-equilibrated Ccl4 system and made two surrounded layer of
water. My system was quickly eqxanded on Z-dimension and slightly shrinked
on X.

I think that such problem could be due to some problems with the vdw radius
value for CCl4. E.g I didnt find this value in the vdwradii.dat file.


James

2012/2/16 Mark Abraham 

>  On 16/02/2012 1:45 AM, James Starlight wrote:
>
> Mark,
>
> I've used that dimensions in accordance to some literature where the same
> membrane-mimicking simulation were performed.
>
> I've tried to rise cutoffs
>
>
> Don't, that breaks your model physics and makes it even more likely you
> will encounter problems with the system dimensions becoming too small for
> the cut-off!
>
>
>  and dicrease integration step but my system have been stil crashed during
> npt.
>
> I'm using
>  pcoupl= Parrinello-Rahman
>
> wich I've found in the KALP tutorial because I have not found the same npt
> example file in the Biphastic tutorial :)
>
>
> So you're following some other work and not copying their equilibration
> protocol and/or model physics?
>
>
> Could you advise me another p_coup algorithm for my Ccl4 system?
>
>
> There's only two choices available. Manual 3.4.9 specifically warns
> against one of them for equilibration. What is there to say?
>
> You should be sure to construct a simple case and get the model physics
> validated. For the moment, forget about all the stuff where you were
> struggling to insert more CCl4 into a box with CCl4 (probably creating a
> far-from-equilibrium starting configuration). Don't try to learn to run on
> stilts while shaving. Learn to shave, then to walk on stilts, then to run,
> then start combining them.
>
> Mark
>
>
>
> James
>
> -- Forwarded message --
> From: Mark Abraham 
> Date: 2012/2/15
> Subject: Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4
> layer
> To: Discussion list for GROMACS users 
>
>
>  On 15/02/2012 4:45 PM, James Starlight wrote:
>
> Mark,
>
>
> due to hight density the volume of my system have been slightly increased
> and during NPT phase I've obtained error
>
> Fatal error:
> One of the box vectors has become shorter than twice the cut-off length or
> box_yy-|box_zy| or box_zz has become smaller than the cut-off.
>
> I'm using 0.9 for electrostatic and 1.4 for vdw cutofs and the dimensions
> of my box was 6.5 3 3 on the initial step and 6.6 3 3.3 before crush :)
>
> I want prevent such expansion of my system by increasing of pressure and/
> or compressibility but I have not found exact sollution yet.
>
>
>  Your system is dangerously small for those cut-offs if your initial
> density is not correct for your model physics. Your y and z dimensions only
> just contain a full cut-off sphere. You should also make sure you are
> following the advice about choice of P-coupling algorithm in manual 3.4.9,
> and consider using a very small integration time step. I remain unconvinced
> by this thread that you have generated a starting configuration that does
> not have atomic clashes.
>
> Mark
>
>
>
>
> James
>
>
> 2012/2/14 Mark Abraham 
>
>>  On 14/02/2012 11:01 PM, James Starlight wrote:
>>
>> This also was solved by the some extra minimisation steps.
>>
>>
>> I've forced with another problem :D
>>
>> During npt equilibration my system have slightly expanded so my desired
>> volume and density were perturbed.
>>
>> I've noticed the below options in npt wich could help me
>>
>> ref_p= 1 1
>> compressibility = 4.5e-5
>>
>>  i'm using this compressibility value   because I'm modelling the
>> lipid-like environment so I think that I must increase pressure.  Could you
>> remind me the dependence of pressure from density and volume for liquids ?
>> :)
>>
>>
>>  Your forcefield, simulation cell contents and .mdp settings will
>> determine the equilibrium density. Whether you need to do anything depends
>> on whether you've made a statistically significant post-equilibration
>> measurement of your average density. Haphazardly increasing the reference
>> pressure for the coupling will reduce the volume, but now you are
>> simulating at that pressure. See
>&

Re: Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

[James Starlight]

So my problem still is

1) During npt without peptide my Ccl4 system expan rapidly in X-dimension.
That produce error on 2nd ns of equilibration

One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.

2) During npt with peptide my system expan rapidly in Z direction ( along
that axe my peptide is oriented) So as concequence I've obtained the same
error.

Possible sollution wich I've found in litterature

1) To fix one dimension of my PB. How I could fix the X dimension of my box
during npt phace of pure Ccl4 and allow only change in 2 other dimensions ?

2) I have not found radius for Cl for Gromos56 ff.
Is this possible to decrease that value during npt phase to obtain system
with desired hight density? What value should I use?

James

2012/2/16 James Starlight 

> Mark,
>
> I'm using exact all parameters wich I found in different experimental work.
>
> By the way reducing of integration step to 1fs provide me with better
> equilibration of the Ccl4 system  ( I've being obtained stabile system
> during 3 ns)
>
> but I had a problems during ntp equilibration when I inserted test peptide
> into that pre-equilibrated Ccl4 system and made two surrounded layer of
> water. My system was quickly eqxanded on Z-dimension and slightly shrinked
> on X.
>
> I think that such problem could be due to some problems with the vdw
> radius value for CCl4. E.g I didnt find this value in the vdwradii.dat file.
>
>
> James
>
>
> 2012/2/16 Mark Abraham 
>
>>  On 16/02/2012 1:45 AM, James Starlight wrote:
>>
>> Mark,
>>
>> I've used that dimensions in accordance to some literature where the same
>> membrane-mimicking simulation were performed.
>>
>> I've tried to rise cutoffs
>>
>>
>> Don't, that breaks your model physics and makes it even more likely you
>> will encounter problems with the system dimensions becoming too small for
>> the cut-off!
>>
>>
>>  and dicrease integration step but my system have been stil crashed
>> during npt.
>>
>> I'm using
>>  pcoupl= Parrinello-Rahman
>>
>> wich I've found in the KALP tutorial because I have not found the same
>> npt example file in the Biphastic tutorial :)
>>
>>
>> So you're following some other work and not copying their equilibration
>> protocol and/or model physics?
>>
>>
>> Could you advise me another p_coup algorithm for my Ccl4 system?
>>
>>
>> There's only two choices available. Manual 3.4.9 specifically warns
>> against one of them for equilibration. What is there to say?
>>
>> You should be sure to construct a simple case and get the model physics
>> validated. For the moment, forget about all the stuff where you were
>> struggling to insert more CCl4 into a box with CCl4 (probably creating a
>> far-from-equilibrium starting configuration). Don't try to learn to run on
>> stilts while shaving. Learn to shave, then to walk on stilts, then to run,
>> then start combining them.
>>
>> Mark
>>
>>
>>
>> James
>>
>> -- Forwarded message --
>> From: Mark Abraham 
>> Date: 2012/2/15
>> Subject: Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4
>> layer
>> To: Discussion list for GROMACS users 
>>
>>
>>  On 15/02/2012 4:45 PM, James Starlight wrote:
>>
>> Mark,
>>
>>
>> due to hight density the volume of my system have been slightly increased
>> and during NPT phase I've obtained error
>>
>> Fatal error:
>> One of the box vectors has become shorter than twice the cut-off length
>> or box_yy-|box_zy| or box_zz has become smaller than the cut-off.
>>
>> I'm using 0.9 for electrostatic and 1.4 for vdw cutofs and the dimensions
>> of my box was 6.5 3 3 on the initial step and 6.6 3 3.3 before crush :)
>>
>> I want prevent such expansion of my system by increasing of pressure and/
>> or compressibility but I have not found exact sollution yet.
>>
>>
>>  Your system is dangerously small for those cut-offs if your initial
>> density is not correct for your model physics. Your y and z dimensions only
>> just contain a full cut-off sphere. You should also make sure you are
>> following the advice about choice of P-coupling algorithm in manual 3.4.9,
>> and consider using a very small integration time step. I remain unconvinced
>> by this thread that you have generated a starting configuration that does
>> not have atomic clashes.
>>
>> 

Re: Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

[James Starlight]

Mark,




The pure Ccl4 cube was expanded in X dimension during npt phase. By the way
I've been able to prevent it by increasing the ref_p of X up to 5 ussing
semiisotropic pcoupltype

By when I've inserted peptide on the npt of that system my Ccl4 box was
expanded on Z rapidly.

Might  this way to increase ref_p be usefull ?

I want to obtain very tightly packet Ccl4 layer with high density
(~1500kg/m^3) to mimick membrane acyl-chain hydrophobic layer

James
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Re: Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

[James Starlight]

By the way I also wounder to know how I could keep my system after
equilibration.


E.g I've equilibrated CCl4+water system and obtain stabile system on
desired timescale.

Than I've used genbox to merge my pre-oriented peptide with the
pre-equilibrated system.

genbox -cp peptide_newbox.gro -cs CCl4_water_box.gro -o peptide_in_box.gro



As the consequence I've obtained system with peptide inserted in CCl4 but
without water layer.

Is there any way to preserve water layer during Genbox peptide insertion?


James
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Re: [gmx-users] Re: Placing ions in the specified positions

[James Starlight]

Dear all :)

I have one extra question about Genion.

I want to neitralise my system with the qtot - 1.550002e by placing some Na
and Cl ions under the physiological concetrantion 100 mmol/l

I've performed

genion -s ions.tpr -o b2ar_ions.gro -p topol.top -pname NA -nname CL -conc
0.1 -neutral

but insytead I've obtained system with 4.499977e-01 changre

What should I do to fix this problem?

James

2012/2/16 Kathleen Kirchner 

> Dear James,
>
> I was working for a longer time on ion placement within more or less
> equilibrated structures. I found my nearly magical miracle solving those
> problems in not using any gromacs tool for producing the input structure
> but rather use the free software Packmol:
>
> http://www.ime.unicamp.br/~**martinez/packmol/
>
> The software solves a mathematical minimization problem instead of putting
> somewhere molecules and deleting others.
>
> After a short energy minimization of the obtained output structure (a few
> 100 steps of steep algorithm) usally my systems work fine.
>
> Best
> Kathleen
>
>
> --
> Kathleen Kirchner
> PhD student
> Max Planck Institute for Mathematics in the Sciences
> (MPI f. Mathematik in den Naturwissenschaften)
> Inselstr. 22-26, D04103 Leipzig
> e-mail: kirch...@mis.mpg.de
> web: 
> http://www.mis.mpg.de/scicomp/**CompPhysChem/
> Tel +49 341 9959 725
> Fax +49 341 9959 999
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
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> http://www.gromacs.org/**Support/Mailing_Lists
>
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[gmx-users] Protonation state of the ionisable residues

[James Starlight]

Dear Gromacs Users!



I'd like to change default protonation state of some specified Glu and Asp
residues im my protein.

By defaylt pdb2gmx -ignh create unprotonated state of the negatively
charged residues but I want to make 2 of such residues protonated to mimick
some intermollecular interactions.

How I could make such edition to my structure ? Is it possible to make such
changing AFTER pdb2gmx processing of my structure ( manually editiong GRO
or PDB file and TOPOLOGY)?


Thanks

James
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Re: [gmx-users] Protonation state of the ionisable residues

[James Starlight]

Thanks Justin.

Your aproach is very usefull indeed.

I've just one relative question about CAPPING of the termi in the case of
simulation of the membrane receptors. In that proteins both of N and C
termi are in the water polar layer. In the literature I've  found nothing
about capping of the termi as well as changing of protonated state of that
fragments. What advantages might have such capping of the termni of that
protein?


James

2012/2/22 Justin A. Lemkul 

>
>
> James Starlight wrote:
>
>> Dear Gromacs Users!
>>
>>
>>
>> I'd like to change default protonation state of some specified Glu and
>> Asp residues im my protein.
>>
>> By defaylt pdb2gmx -ignh create unprotonated state of the negatively
>> charged residues but I want to make 2 of such residues protonated to mimick
>> some intermollecular interactions.
>>
>> How I could make such edition to my structure ? Is it possible to make
>> such changing AFTER pdb2gmx processing of my structure ( manually editiong
>> GRO or PDB file and TOPOLOGY)?
>>
>>
> It is possible, but would be an extreme hassle and would be very
> error-prone. You'd have to add in the new atoms, renumber *all* subsequent
> bonded and nonbonded interactions.
>
> The better approach is to re-create the topology with pdb2gmx -asp -glu.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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[gmx-users] Internal water in the membrane receptor

[James Starlight]

Dear Gromacs Users!

I want to perform simulation of the membrane receptor in the membtane
environment. There are some evidence about precense of the
functional-relevant internal water mollecules in the transmembrane
alpha-helix bundle of the receptor.


I want to take into account that internal water in my model. I have
coordinates of the X-ray structures wich have all that water. Also I have
perfect model of the same protein wich have not that water but have
full-length structure ( there are some missing residues in the X-ray
structures- e.g in the loop regions).

So what the best way to build system would  be in my case?

1-  Should I use X-ray structure where internal water has already present
and build missing loops via model software ? How I could preserve the
internal waters in that starting structure when this structure will be
processed by pdb2gmx ?

2- Or the best way is to incorporate all waters in the model of my protein
? If this aproach could be better what is the simplest way to transfer
exact coordinates of water in that holo model ? )

Thanks for help


James
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[gmx-users] Re: Internal water in the membrane receptor

[James Starlight]

Up! :)

Please provide me with the best sollution of my problem! I just want to
copy some water mollecules from X-ray structure to my model and place it in
the identical possitions inside the TM budle of my protein.  What are the
most trivial way to solve this task?

James

2012/2/22 James Starlight 

> Dear Gromacs Users!
>
> I want to perform simulation of the membrane receptor in the membtane
> environment. There are some evidence about precense of the
> functional-relevant internal water mollecules in the transmembrane
> alpha-helix bundle of the receptor.
>
>
> I want to take into account that internal water in my model. I have
> coordinates of the X-ray structures wich have all that water. Also I have
> perfect model of the same protein wich have not that water but have
> full-length structure ( there are some missing residues in the X-ray
> structures- e.g in the loop regions).
>
> So what the best way to build system would  be in my case?
>
> 1-  Should I use X-ray structure where internal water has already present
> and build missing loops via model software ? How I could preserve the
> internal waters in that starting structure when this structure will be
> processed by pdb2gmx ?
>
> 2- Or the best way is to incorporate all waters in the model of my protein
> ? If this aproach could be better what is the simplest way to transfer
> exact coordinates of water in that holo model ? )
>
> Thanks for help
>
>
> James
>
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Re: [gmx-users] Re: Internal water in the membrane receptor

[James Starlight]

Mark,

what about the next sollution

firstly I'll align both of my structures ( x-ray with water and another my
model without water)

than I'll copy aligned water from first structure to my model in the bottom
of the GRO file.

than I'll minimise this editted structure to relax side chains of the
residues wich are in contact with the new waters

Might this aproach be usefull? Commonly I use it to prepare protein-ligand
complexes.

James

2012/2/24 Mark Abraham 

>  On 24/02/2012 6:31 PM, James Starlight wrote:
>
> Up! :)
>
> Please provide me with the best sollution of my problem! I just want to
> copy some water mollecules from X-ray structure to my model and place it in
> the identical possitions inside the TM budle of my protein.  What are the
> most trivial way to solve this task?
>
>
> You have a non-trivial problem. You can either build the model on the
> structure that has the waters (pdb2gmx doesn't strip water, IIRC), or work
> out some geometric criteria for placing the waters afterwards. Not every
> problem has an existing tool for its solution.
>
> Mark
>
>
>
> James
>
> 2012/2/22 James Starlight 
>
>> Dear Gromacs Users!
>>
>> I want to perform simulation of the membrane receptor in the membtane
>> environment. There are some evidence about precense of the
>> functional-relevant internal water mollecules in the transmembrane
>> alpha-helix bundle of the receptor.
>>
>>
>> I want to take into account that internal water in my model. I have
>> coordinates of the X-ray structures wich have all that water. Also I have
>> perfect model of the same protein wich have not that water but have
>> full-length structure ( there are some missing residues in the X-ray
>> structures- e.g in the loop regions).
>>
>> So what the best way to build system would  be in my case?
>>
>> 1-  Should I use X-ray structure where internal water has already present
>> and build missing loops via model software ? How I could preserve the
>> internal waters in that starting structure when this structure will be
>> processed by pdb2gmx ?
>>
>> 2- Or the best way is to incorporate all waters in the model of my
>> protein ? If this aproach could be better what is the simplest way to
>> transfer exact coordinates of water in that holo model ? )
>>
>> Thanks for help
>>
>>
>> James
>>
>
>
>
>
>
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Re: [gmx-users] Re: Internal water in the membrane receptor

[James Starlight]

Mark,


So as I understood the ussage of X-ray structure as the starting model
where the internal water is already present might be good in case to avoid
those sterric issues doesn't it ?

What are additional options should I use for preparation of such system
with pdb2gmx ? Should I use posres on the internal water  ( e.g on oxygen
atoms) during energy minimisation and equilibration phases?


James


2012/2/24 Mark Abraham 

>
>  Might work, but there are lots of steric issues and potential problems.
>
> Mark
>
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Re: [gmx-users] Re: Internal water in the membrane receptor

[James Starlight]

Today I've tried to model internal water and forced with some problems :)

I've built my system by transferring water from X-ray structure to my
model. Than I've minimized this new structure in vacuum and water still
present on the desired positions

1) But when I've made my complete system ( with membrane mimicking Ccl4
layer) I've obtained this strange error during MDrun of this whole system (
there are no any errors during gromp pre-processing)

Fatal error:
The [molecules] section of your topology specifies more than one block of
a [moleculetype] with a [settles] block. Only one such is allowed. If you
are trying to partition your solvent into different *groups* (e.g. for
freezing, T-coupling, etc.) then you are using the wrong approach. Index
files specify groups. Otherwise, you may wish to change the least-used
block of molecules with SETTLE constraints into 3 normal constraints.


My topology has the below constracton

[ molecules ]
; Compound#mols
Protein 1
XW  16
Ccl4804
SOL 9884

where XW is the new .itp made for internal water based on SPC.itp

I dont know what exactly this strange error means and how to fix it :(


2) Also when I've changed protonation state of two ASP residues all
internal water left protein interior diffusing in the interiour during in
vacuum minimisation :)
I've tried to apply POSRES of that internal water but another eror occur

[ file posre_XW.itp, line 5 ]:
Atom index (4229) in position_restraints out of bounds (1-3).
This probably means that you have inserted topology section
"position_restraints"

I've checked posre_XW.itp file and didnt find any errors! The atom numbers
in posres are correspond to the atom nymbers in the GRO file. Why this
error might occur?

my topology
; Include X-ray water topology
#include "XW.itp"

; Include Position restraint for XW
#ifdef POSRES_XW
#include "posre_XW.itp"
#endif

my mdp
define= -DPOSRES_XW
integrator= steep

James

2012/2/25 Mark Abraham 

> On 25/02/2012 5:37 AM, James Starlight wrote:
>
>> Mark,
>>
>>
>> So as I understood the ussage of X-ray structure as the starting model
>> where the internal water is already present might be good in case to avoid
>> those sterric issues doesn't it ?
>>
>
> Yes. This was one of the options I suggested earlier.
>
>
>
>> What are additional options should I use for preparation of such system
>> with pdb2gmx ? Should I use posres on the internal water  ( e.g on oxygen
>> atoms) during energy minimisation and equilibration phases?
>>
>
> You probably do want a contiguous block of atoms with position restraints.
> That will require you have two different [moleculetype] sections for the
> different "kinds" of water, since the [position_restraints] section applies
> to all instances of its [moleculetype], and you will need to disable
> [settle] for at least one of those. It might be easier not to use separate
> restraints for a subset of water.
>
> Mark
>
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Re: [gmx-users] Re: Internal water in the membrane receptor

[James Starlight]

Justin,

2012/2/25 Justin A. Lemkul 

>
>
>
> You likely have a [settles] directive applied the the XW molecules
> (crystal waters, yes?) and SOL.  You can't do that.  The block of molecules
> to which [settles] are applied must be continuous.  You'll have to replace
> the [settles] directive in XW with normal constraints.
>

Yes, this works! Thanks alot.
I only wounder to know should I delete
[ exclusions ] from the itp of my X-ray water or not ? This directive is
linked with the [settles] by the if expression so I've replaced it too.


>
> Your numbering is wrong.  Numbering within a [position_restraints]
> directive has nothing to do with the .gro file, and is based on the
> numbering of the atoms in a [moleculetype].
>
>
> It's clear now. As I understtod the  [moleculetype] of the restricted
molecule must be in FIRST place in my topol.top file but in that file the
PROTEIN at first place instead. How I could make this changing in my
multi-topology file ? I've tried to place

; Include X-ray water topology
#include "XW.itp"

; Include Position restraint for XW
#ifdef POSRES_XW
#include "posre_XW.itp"
#endif

at the begining of the topol.top file. But the error during grompt was the
same about wrong atom order :(


James
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Re: [gmx-users] Re: Internal water in the membrane receptor

[James Starlight]

Mark,

I've found a possible sollution to restrict oxygens of my X-ray water by
possible plasing the below string in the TOPOLOGY.top of my system

; Include X-ray water topology
#include "XW.itp"

; Include Position restraint file
#ifdef POSRES_XW
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

I havent recieved any errors from gromp. Does this aproach correct in
general ?

I dont know why but after minimisation constrained mollecules were diffused
from the protein interious so POSRES have not worked :(

My minim.mdp consist of two separate posres for water as well as for ligand
groups ( there are no posre for protein).


define= -DPOSRES_LIG -DPOSRES_XW; position restrain the protein
integrator= steep; Algorithm (steep = steepest descent
minimization)
emtol= 1000.0  ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps= 5  ; Maximum number of (minimization) steps to
perform
energygrps = Protein CAR

What should I add to that file to activate posres?
Finally are the constraints algorithm needed here ?


James
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[gmx-users] Distance between selected atoms during simulation

[James Starlight]

Dear Gromacs Users!


I want to perform measurements of the distances between backbone as well as
side-chain atoms of the selected residues using gro and trajectory files.

What Gromacs program should I use for such measurements?


James
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[gmx-users] Generation of the Distance Restraints

[James Starlight]

Dear Gromacs users!


I want to perform constrained MD simulation of my protein with inclusion of
some experimental restraints.


1) I found that genrest cpmmand could be usefull for the generation of the
distance restrictions wich I could use in my constrined simulation.

Also in manual I've found that command like

genrestr -f b2ar.gro -disre -index.ndx -o test.itp

will produce some distance restricted matrix of the whole groups presented
in the index.ndx file.

So how I could select to contrain selected residues within selected
distance by means the index file?  E.g I've manually point out 2 residues
in index.ndx. I waant to preserve between that residues some desired
distance D wich I've obtaine from the experimental data. How I could do it
via genrestr and waht addition flags should I use for that purpose ?


2) Is there any way to apply gradually the desired dist.resrs during MDrun
to prevent some artifacts in my system wich would occur due to the rapid
application of the dis.res ( e.g in cases where the conformation of the
started structure and that wich I'd obtained fter application of the
restrains are slightly different)?

Thanks for help,


James
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Re: [gmx-users] Generation of the Distance Restraints

[James Starlight]

Francesca,

Yes I suppose this is good aproach for the generation of position
restricktions on the desired atoms. But I want to restrain the distance
between selected pairs of atoms ( e.g between C-alpha- C-alpha atoms of two
different residues).

Also I want to restrain some dihedral angles in the desired rotameric forms.

In literature I've found that peple have dome the same things in Gromacs
but I could not find detailed algorithm of such methodology :(

James

12 марта 2012 г. 18:05 пользователь francesca vitalini <
francesca.vitalin...@gmail.com> написал:

> I think you can make an index file using make_ndx where you specify
> the atoms you want to restraint.
> Hope this can help.
> Francesca
>
> 2012/3/12 James Starlight :
> > Dear Gromacs users!
> >
> >
> > I want to perform constrained MD simulation of my protein with inclusion
> of
> > some experimental restraints.
> >
> >
> > 1) I found that genrest cpmmand could be usefull for the generation of
> the
> > distance restrictions wich I could use in my constrined simulation.
> >
> > Also in manual I've found that command like
> >
> > genrestr -f b2ar.gro -disre -index.ndx -o test.itp
> >
> > will produce some distance restricted matrix of the whole groups
> presented
> > in the index.ndx file.
> >
> > So how I could select to contrain selected residues within selected
> distance
> > by means the index file?  E.g I've manually point out 2 residues in
> > index.ndx. I waant to preserve between that residues some desired
> distance D
> > wich I've obtaine from the experimental data. How I could do it via
> genrestr
> > and waht addition flags should I use for that purpose ?
> >
> >
> > 2) Is there any way to apply gradually the desired dist.resrs during
> MDrun
> > to prevent some artifacts in my system wich would occur due to the rapid
> > application of the dis.res ( e.g in cases where the conformation of the
> > started structure and that wich I'd obtained fter application of the
> > restrains are slightly different)?
> >
> > Thanks for help,
> >
> >
> > James
> >
> > --
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Re: [gmx-users] Generation of the Distance Restraints

[James Starlight]

Mark, Justin,

Thanks for advises. Indeed I think that simple text editor would be better
sollution in my casw because of small number of restraints.

I just have a question about definition of the Distances

This is the default of the restraints between atom 10 and 16.

[ distance_restraints ]
; ai aj type index type' low up1 up2 fac
  10 16 10 1 0.0 0.3 0.4 1.0



I'd like to restrict distance between both of that atoms   7.96 < r(Ca-Ca)<
8.41

I've found that the up1 is the 7.96 and up2 is the 8.41 but how I could
specify 'low' in the above table ? Should I obtain value for the initial
Ca-Ca distance between my residues from the initial structure? How I could
do it?


James






12 марта 2012 г. 18:38 пользователь Justin A. Lemkul написал:

>
>
> James Starlight wrote:
>
>> Francesca,
>>
>> Yes I suppose this is good aproach for the generation of position
>> restricktions on the desired atoms. But I want to restrain the distance
>> between selected pairs of atoms ( e.g between C-alpha- C-alpha atoms of two
>> different residues).
>>
>>
> How many restraints do you need to create?  If they are this simple, you
> can write them yourself using a text editor in conjunction with manual
> section 4.3.4.  Using genrestr is only really helpful when you require a
> network of distance restraints between the atoms of a given group.  If
> there are only a few to create, it's actually more work to use make_ndx and
> genrestr than it is to fire up your favorite text editor.
>
>
>  Also I want to restrain some dihedral angles in the desired rotameric
>> forms.
>>
>>
> See manual section 4.3.3 and http://www.gromacs.org/**
> Documentation/How-tos/**Dihedral_Restraints<http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints>
> .
>
>
>  In literature I've found that peple have dome the same things in Gromacs
>> but I could not find detailed algorithm of such methodology :(
>>
>>
> All relevant equations are provided in the manual, and examples are
> provided either there or on the Gromacs site.  If you need further
> information, ask a specific question related to what you can't find or
> don't understand.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
>
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Re: [gmx-users] Generation of the Distance Restraints

[James Starlight]

Justin,

1) I've already tried to examine this graphs but have not understood the
meaning of the Ro value.

E.g I have known distance restrains for the pair of residue wich are 1написал:

>
>
> James Starlight wrote:
>
>> Mark, Justin,
>>
>> Thanks for advises. Indeed I think that simple text editor would be
>> better sollution in my casw because of small number of restraints.
>>
>> I just have a question about definition of the Distances
>>
>> This is the default of the restraints between atom 10 and 16.
>>
>> [ distance_restraints ]
>> ; ai aj type index type' low up1 up2 fac
>>  10 16 10 1 0.0 0.3 0.4 1.0
>>
>>
>>
>> I'd like to restrict distance between both of that atoms   7.96 <
>> r(Ca-Ca)< 8.41
>>
>> I've found that the up1 is the 7.96 and up2 is the 8.41 but how I could
>> specify 'low' in the above table ? Should I obtain value for the initial
>> Ca-Ca distance between my residues from the initial structure? How I could
>> do it?
>>
>>
> See Figure 4.13 and equations 4.79 in the manual.  r0 = low, r1 = up1, and
> r2 = up2.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
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Re: [gmx-users] Generation of the Distance Restraints

[James Starlight]

Mark,



> Anything else you've known and understood about distance restraints in
> some unknown context doesn't matter. What's written in the GROMACS
> manual matters for using them in GROMACS :-)
>

So because I'm not quite understood those equations I could not
properly define my restrains (wich are in the form presented in mu
example in previous message) in accordance to the form presented in
Gromac's manual. i think it'll be kindly from you to provide the
Gromacs restrain section
(http://www.gromacs.org/Documentation/How-tos/Distance_Restraints)
with some more detailed example of application of such disres.  It's
not quite understtod how the values 0 0.3 and 0.4 are correspond to
the real restrains wich would be obtained from experimental data (
Commonly it's single value of the some range like 0.4
> I already answered this.
> http://lists.gromacs.org/pipermail/gmx-users/2012-March/069301.html

I've found only theoretical explanation of such possibility (
gradually increasing force constant during simulation). But I
intresting in practical implementation. Could I do it in scope of
single MDrun by some options in mdm fle or should I do step-by-step
series of simulation with gradually changing forces appplied on the
disres in each MDrun?


James
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Re: [gmx-users] Generation of the Distance Restraints

[James Starlight]

Mark, thanks for explanation.

So if I understood that graph correctly I must define R1=1 and R2=2 values
from my example 1написал:

>
>
> I can't think of a clearer way to explain the functional form of the
> distance restraint than the given equation with an example graph of it
> nearby. You have some distance range that you want to see happen based on
> some external information. You need to choose the distance constants for
> that functional form to reproduce that in a way that you judge will work,
> given your initial distance. The linear regime above r_2 is useful for not
> having forces that are massively large (from a quadratic potential) far
> from the region of zero potential. Whether this is important depends on
> your starting configuration.
>
>
>
>>
>>  I already answered this.
>>> http://lists.gromacs.org/**pipermail/gmx-users/2012-**March/069301.html
>>>
>> I've found only theoretical explanation of such possibility (
>> gradually increasing force constant during simulation). But I
>> intresting in practical implementation. Could I do it in scope of
>> single MDrun by some options in mdm fle or should I do step-by-step
>> series of simulation with gradually changing forces appplied on the
>> disres in each MDrun?
>>
>
> Only step by step. Something like simulated annealing is only available
> for temperature variation.
>
> Mark
>
>>
>>
>> James
>>
>
> --
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Re: [gmx-users] Generation of the Distance Restraints

[James Starlight]

It's appeared two new questions on the same topic :)

1) By the way, new error have been occured when I've tried to use
multi-core station with MPI to calculate such restrained model ( I have no
same problems on the single station )

the error

Fatal error:
Time or ensemble averaged or multiple pair distance restraints do not work
(yet$
For more information and tips for troubleshooting, please check the GROMACS

What should I do to fix it ?
I've made my restrained on the basis of example presented in the manual
section.

2) Also I've found that there is more simple way to define restraines based
on the BONDS enty in the topology file. Could you provide me with the more
information about this simpler way ?

Thanks for help again,


James

14 марта 2012 г. 10:50 пользователь James Starlight
написал:

> Mark, thanks for explanation.
>
> So if I understood that graph correctly I must define R1=1 and R2=2 values
> from my example 1 distance range ( from 1 to 2 angstr). In other words this would restrains
> the i and j atom to the desired distance by the force wich would increased
> by the quadratic progresion upon distance will increased up to 2. Does it
> correct ?
>
> So the value R0 ( no forces= no restraints) must correspond to the values
> above and below my range. How the same range value for R0 could be defined ?
>
>
> JAmes
>
> 14 марта 2012 г. 3:42 пользователь Mark Abraham 
> написал:
>
>
>>
>> I can't think of a clearer way to explain the functional form of the
>> distance restraint than the given equation with an example graph of it
>> nearby. You have some distance range that you want to see happen based on
>> some external information. You need to choose the distance constants for
>> that functional form to reproduce that in a way that you judge will work,
>> given your initial distance. The linear regime above r_2 is useful for not
>> having forces that are massively large (from a quadratic potential) far
>> from the region of zero potential. Whether this is important depends on
>> your starting configuration.
>>
>>
>>
>>>
>>>  I already answered this.
>>>> http://lists.gromacs.org/**pipermail/gmx-users/2012-**March/069301.html<http://lists.gromacs.org/pipermail/gmx-users/2012-March/069301.html>
>>>>
>>> I've found only theoretical explanation of such possibility (
>>> gradually increasing force constant during simulation). But I
>>> intresting in practical implementation. Could I do it in scope of
>>> single MDrun by some options in mdm fle or should I do step-by-step
>>> series of simulation with gradually changing forces appplied on the
>>> disres in each MDrun?
>>>
>>
>> Only step by step. Something like simulated annealing is only available
>> for temperature variation.
>>
>> Mark
>>
>>>
>>>
>>> James
>>>
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before
>>  posting!
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>>
>
>
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Fwd: [gmx-users] Generation of the Distance Restraints

[James Starlight]

Mark,


My restrains on topology consist of the next section

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

[ dihedral_restraints ]
; ai   ajakal  type  label  phi  dphi  kfac  power
; Chi N - CA - CB - CG
  29082910 29112912 1  1  180 0 1  2

[ distance_restraints ]
; ai aj type index type' low up1 up2 fac
  1097 3201 11 1 0.796 0.841 0.900 1.0
  2948 3201 12 1 0.796 0.841 0.900 1.0
  1097 2948 13 1 0.796 0.841 0.900 1.0
  1097 2999 14 1 0.800 1.000 1.100 1.0
  1098 2034 15 1 0.800 1.000 1.100 1.0
  1098 2042 16 1 0.800 1.000 1.100 1.0
  1098 2067 17 1 0.800 1.000 1.100 1.0
  1130 3241 18 1 0.540 0.630 0.700 1.0
  546  3393 19 1 1.162 1.725 1.800 1.0
  628  3460 110 1 1.438 2.067 2.100 1.0
  637  3460 111 1 0.700 1.238 1.300 1.0
  648  2791 112 1 1.788 2.152 2.200 1.0
  648  3376 113 1 1.736 2.061 2.150 1.0
  2292 2743 114 1 0.200 0.300 0.350 1.0
  1258 2203 115 1 0.200 0.300 0.350 1.0

Also I've attached my md.mdp file.

I have no problems with that system on my home desktop.

On cluster with installed MPI I've lunch my simulation by means of below
command

grompp -f md.mdp -c nvtWprotonated.gro -p topol.top -n index.ndx -o
md_50ns.tpr

mpiexec -np 24 mdrun_mpi_d.openmpi -v -deffnm md_50ns


I'll be very thankful if you show me what's wrong could be with my initial
systems because I have no any problems with my systems on my home desktop.
On the other hand on Cluster some of my jobs ends with the errors (
something wrong with PME order or the error wich I've shown you with the
ensembles of restrains)

It was installed the same last version of Gromacs on cluster like on my
desctop ( difference only in double precission with lack on my home desctop
but present on cluster)

Could you tell me in what log files I could obtain more detailed
information of the source of such erors? I've checked only md.log as well
as name_of_the_simulation.log. Besides there are files gromacs.err wich
contain information about crashed simulation.



Thanks for help again,


James

14 марта 2012 г. 16:10 пользователь Mark Abraham
написал:

>  You're probably doing something wrong, but in the absence of a command
> line and your .top file fragment, we can't possibly know.
>
>
> Mark
>
>
>
> Thanks for help again,
>
>
> James
>
> 14 марта 2012 г. 10:50 пользователь James Starlight <
> jmsstarli...@gmail.com> написал:
>
>> Mark, thanks for explanation.
>>
>> So if I understood that graph correctly I must define R1=1 and R2=2
>> values from my example 1> my distance range ( from 1 to 2 angstr). In other words this would
>> restrains the i and j atom to the desired distance by the force wich would
>> increased by the quadratic progresion upon distance will increased up to 2.
>> Does it correct ?
>>
>> So the value R0 ( no forces= no restraints) must correspond to the values
>> above and below my range. How the same range value for R0 could be defined ?
>>
>>
>> JAmes
>>
>> 14 марта 2012 г. 3:42 пользователь Mark Abraham 
>> написал:
>>
>>
>>>
>>> I can't think of a clearer way to explain the functional form of the
>>> distance restraint than the given equation with an example graph of it
>>> nearby. You have some distance range that you want to see happen based on
>>> some external information. You need to choose the distance constants for
>>> that functional form to reproduce that in a way that you judge will work,
>>> given your initial distance. The linear regime above r_2 is useful for not
>>> having forces that are massively large (from a quadratic potential) far
>>> from the region of zero potential. Whether this is important depends on
>>> your starting configuration.
>>>
>>>
>>>
>>>>
>>>>  I already answered this.
>>>>> http://lists.gromacs.org/pipermail/gmx-users/2012-March/069301.html
>>>>>
>>>> I've found only theoretical explanation of such possibility (
>>>> gradually increasing force constant during simulation). But I
>>>> intresting in practical implementation. Could I do it in scope of
>>>> single MDrun by some options in mdm fle or should I do step-by-step
>>>> series of simulation with gradually changing forces appplied on the
>>>> disres in each MDrun?
>>>>
>>>
>>>  Only step by step. Something like simulated annealing is only available
>>> for temperature variatio

Re: Fwd: [gmx-users] Generation of the Distance Restraints

[James Starlight]

Justin,

The whole error was

Reading file md_rest1.tpr, VERSION 4.5.5 (single precision)

NOTE: atoms involved in distance restraints should be within the longest
cut-of$


---
Program mdrun_mpi_d.openmpi, VERSION 4.5.5
Source code file: /tmp/build/gromacs-4.5.5/src/gmxlib/disre.c, line: 143

Fatal error:
Time or ensemble averaged or multiple pair distance restraints do not work
(yet$
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"Gabba Gabba Hey!" (The Ramones)

Error on node 5, will try to stop all the nodes
Halting parallel program mdrun_mpi_d.openmpi on CPU 5 out of 12

---

and so on for each CPU :)

Might it be with some PME order ? I've recieved errors about wrong PME
order when tried to lauch my simulations on big ammoun of the nodes but
could not find possible way to fix it :(


James

14 марта 2012 г. 19:43 пользователь Justin A. Lemkul написал:

>
>
> James Starlight wrote:
>
>> Mark,
>>
>>
>> My restrains on topology consist of the next section
>>
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "posre.itp"
>> #endif
>>
>> [ dihedral_restraints ]
>> ; ai   ajakal  type  label  phi  dphi  kfac  power
>> ; Chi N - CA - CB - CG
>>  29082910 29112912 1  1  180 0 1  2
>>
>> [ distance_restraints ]
>> ; ai aj type index type' low up1 up2 fac
>>  1097 3201 11 1 0.796 0.841 0.900 1.0
>>  2948 3201 12 1 0.796 0.841 0.900 1.0
>>  1097 2948 13 1 0.796 0.841 0.900 1.0
>>  1097 2999 14 1 0.800 1.000 1.100 1.0
>>  1098 2034 15 1 0.800 1.000 1.100 1.0
>>  1098 2042 16 1 0.800 1.000 1.100 1.0
>>  1098 2067 17 1 0.800 1.000 1.100 1.0
>>  1130 3241 18 1 0.540 0.630 0.700 1.0
>>  546  3393 19 1 1.162 1.725 1.800 1.0
>>  628  3460 110 1 1.438 2.067 2.100 1.0
>>  637  3460 111 1 0.700 1.238 1.300 1.0
>>  648  2791 112 1 1.788 2.152 2.200 1.0
>>  648  3376 113 1 1.736 2.061 2.150 1.0
>>  2292 2743 114 1 0.200 0.300 0.350 1.0
>>  1258 2203 115 1 0.200 0.300 0.350 1.0
>>
>> Also I've attached my md.mdp file.
>>
>> I have no problems with that system on my home desktop.
>>
>> On cluster with installed MPI I've lunch my simulation by means of below
>> command
>>
>> grompp -f md.mdp -c nvtWprotonated.gro -p topol.top -n index.ndx -o
>> md_50ns.tpr
>>
>> mpiexec -np 24 mdrun_mpi_d.openmpi -v -deffnm md_50ns
>>
>>
>> I'll be very thankful if you show me what's wrong could be with my
>> initial systems because I have no any problems with my systems on my home
>> desktop. On the other hand on Cluster some of my jobs ends with the errors
>> ( something wrong with PME order or the error wich I've shown you with the
>> ensembles of restrains)
>>
>> It was installed the same last version of Gromacs on cluster like on my
>> desctop ( difference only in double precission with lack on my home desctop
>> but present on cluster)
>>
>> Could you tell me in what log files I could obtain more detailed
>> information of the source of such erors? I've checked only md.log as well
>> as name_of_the_simulation.log. Besides there are files gromacs.err wich
>> contain information about crashed simulation.
>>
>>
>>
> You didn't include the whole error in your first message, which should
> read "Time or ensemble averaged or multiple pair distance restraints do not
> work (yet) with domain decomposition, use particle decomposition (mdrun
> option -pd)"
>
> Thus the error message tells you how to proceed.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
> --
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> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://ww

[gmx-users] Problems with simulation on multi-nodes cluster

[James Starlight]

Dear Gromacs Users!


I have some problems with running my simulation on multi-modes station wich
use open_MPI

I've launch my jobs by means of that script. The below example of running
work on 1 node ( 12 cpu).

#!/bin/sh
#PBS -N gromacs
#PBS -l nodes=1:red:ppn=12
#PBS -V
#PBS -o gromacs.out
#PBS -e gromacs.err

cd /globaltmp/xz/job_name
grompp -f md.mdp -c nvtWprotonated.gro -p topol.top -n index.ndx -o job.tpr
mpiexec -np 12 mdrun_mpi_d.openmpi -v -deffnm job

All nodes of my cluster consist of 12 CPU. When I'm using just 1 node on
that cluster I have no problems with running of my jobs but when I try to
use more than one nodes I've obtain error ( the example is attached in the
gromacs.err file as well as mmd.mdp of that system). Another outcome of
such multi-node simulation is that my job has been started but no
calculation were done ( the name_of_my_job.log file was empty and no update
of .trr file was seen ). Commonly this error occurs when I uses many nodes
(8-10) Finally sometimes I've obtain some errors with the PME order ( this
time I've used 3 nodes). The exactly error differs when I varry the number
of nodes.


Could you tell me whats wrong could be with my cluster?

Thanks for help

James


gromacs.err
Description: Binary data


md.mdp
Description: Binary data
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Re: [gmx-users] Generation of the Distance Restraints

[James Starlight]

Mark,

thanks again for explanation



> The force is the negative of the derivative of the potential with respect
> to the distance. So the force is also zero between r_0 and r_1. So if you
> want a distance to be restrained between 1 and 2 nm, set r_0=1 and r_1=2.
> That way the force is zero if the distance is satisfactory, and non-zero
> when it is not.
>

I'm not quite understood the restrains definition in that case :( So in the
above example the distance between 1 and 2 nm would be restrained and in
accordance to the graph the forces will be zero. But in the range below 1
and 2 nm the forces would be increased in quadratic progression. So if I
understood correctly only when atoms are not in the desired distance range
forces will occur that must bring atoms to the desired distance. This is
the opposite to the position restrains where the forses are constant to
prevent movement of the atoms. Does it correct?

>
>
>
I leave the choice of r_2 to you as an exercise
>

So as I understood the forces occured after r_2 threshold must be extremely
hight in comparison to gradually parabolic rise in the two others
thresholds. In what exacly cases this rapid increase must be usefull in
comparison to the gradually parabolic manner?

Thanks again

James

>
>
> Mark
>
>
>  I must define R1=1 and R2=2 values from my example 1 quadratic restrain forces done in my distance range ( from 1 to 2 angstr).
> In other words this would restrains the i and j atom to the desired
> distance by the force wich would increased by the quadratic progresion upon
> distance will increased up to 2. Does it correct ?
>
> So the value R0 ( no forces= no restraints) must correspond to the values
> above and below my range. How the same range value for R0 could be defined ?
>
>
> JAmes
>
> 14 марта 2012 г. 3:42 пользователь Mark Abraham 
> написал:
>
>>
>>
>> I can't think of a clearer way to explain the functional form of the
>> distance restraint than the given equation with an example graph of it
>> nearby. You have some distance range that you want to see happen based on
>> some external information. You need to choose the distance constants for
>> that functional form to reproduce that in a way that you judge will work,
>> given your initial distance. The linear regime above r_2 is useful for not
>> having forces that are massively large (from a quadratic potential) far
>> from the region of zero potential. Whether this is important depends on
>> your starting configuration.
>>
>>
>>
>>>
>>>  I already answered this.
 http://lists.gromacs.org/pipermail/gmx-users/2012-March/069301.html

>>> I've found only theoretical explanation of such possibility (
>>> gradually increasing force constant during simulation). But I
>>> intresting in practical implementation. Could I do it in scope of
>>> single MDrun by some options in mdm fle or should I do step-by-step
>>> series of simulation with gradually changing forces appplied on the
>>> disres in each MDrun?
>>>
>>
>>  Only step by step. Something like simulated annealing is only available
>> for temperature variation.
>>
>> Mark
>>
>>>
>>>
>>> James
>>>
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
>
>
> --
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Re: [gmx-users] Problems with simulation on multi-nodes cluster

[James Starlight]

Mark, Peter,


I've tried to do .tpr file on my local CPU and launch only

mpiexec -np 24 mdrun_mpi_d.openmpi -v -deffnm MD_100

on the cluster with 2 nodes.

I see my job as working but when I've checking the MD_100.log (attached)
file there are no any information about simulation steps in that file (
when I use just one node I see in that file step-by-step progression of my
simulation like below wich was find in the same log file for ONE NODE
simulation ):

Started mdrun on node 0 Thu Mar 15 11:22:35 2012

   Step   Time Lambda
  00.00.0

Grid: 12 x 9 x 12 cells
   Energies (kJ/mol)
   G96AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
1.32179e+043.27485e+032.53267e+034.06443e+026.15315e+04
LJ (SR)LJ (LR)  Disper. corr.   Coulomb (SR)   Coul. recip.
4.12152e+04   -5.51788e+03   -1.70930e+03   -4.54886e+05   -1.46292e+05
 Dis. Rest. D.R.Viol. (nm) Dih. Rest.  PotentialKinetic En.
2.14240e-023.46794e+001.33793e+03   -4.84889e+059.88771e+04
   Total Energy  Conserved En.Temperature Pres. DC (bar) Pressure (bar)
   -3.86012e+05   -3.86012e+053.11520e+02   -1.14114e+023.67861e+02
   Constr. rmsd
3.75854e-05

   Step   Time Lambda
   20004.00.0

   Energies (kJ/mol)
   G96AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
1.31741e+043.25280e+032.58442e+033.51371e+026.15913e+04
LJ (SR)LJ (LR)  Disper. corr.   Coulomb (SR)   Coul. recip.
4.16349e+04   -5.53474e+03   -1.70930e+03   -4.56561e+05   -1.46485e+05
 Dis. Rest. D.R.Viol. (nm) Dih. Rest.  PotentialKinetic En.
4.78276e+013.38844e+009.82735e+00   -4.87644e+059.83280e+04
   Total Energy  Conserved En.Temperature Pres. DC (bar) Pressure (bar)
   -3.89316e+05   -3.87063e+053.09790e+02   -1.14114e+027.25905e+02
   Constr. rmsd
1.88008e-05

end etc...



What's wrong can be with multi-node computations?


James


15 марта 2012 г. 11:25 пользователь Mark Abraham
написал:

> On 15/03/2012 6:13 PM, Peter C. Lai wrote:
>
>> Try separating your grompp run from your mpirun:
>> You should not really be having the scheduler execute the grompp. Run
>> your grompp step to generate a .tpr either on the head node or on your
>> local
>> machine (then copy it over to the cluster).
>>
>
> Good advice.
>
>
>> (The -p that the scheduler is complaining about only appears in the grompp
>> step, so don't have the scheduler run it).
>>
>
> grompp is running successfully, as you can see from the output
>
> I think "mpiexec -np 12" is being interpreted as "mpiexec -n 12 -p", and
> the process of separating the grompp stage from the mdrun stage would help
> make that clear - read documentation first, however.
>
> Mark
>
>
>
>>
>> On 2012-03-15 10:04:49AM +0300, James Starlight wrote:
>>
>>> Dear Gromacs Users!
>>>
>>>
>>> I have some problems with running my simulation on multi-modes station
>>> wich
>>> use open_MPI
>>>
>>> I've launch my jobs by means of that script. The below example of running
>>> work on 1 node ( 12 cpu).
>>>
>>> #!/bin/sh
>>> #PBS -N gromacs
>>> #PBS -l nodes=1:red:ppn=12
>>> #PBS -V
>>> #PBS -o gromacs.out
>>> #PBS -e gromacs.err
>>>
>>> cd /globaltmp/xz/job_name
>>> grompp -f md.mdp -c nvtWprotonated.gro -p topol.top -n index.ndx -o
>>> job.tpr
>>> mpiexec -np 12 mdrun_mpi_d.openmpi -v -deffnm job
>>>
>>> All nodes of my cluster consist of 12 CPU. When I'm using just 1 node on
>>> that cluster I have no problems with running of my jobs but when I try to
>>> use more than one nodes I've obtain error ( the example is attached in
>>> the
>>> gromacs.err file as well as mmd.mdp of that system). Another outcome of
>>> such multi-node simulation is that my job has been started but no
>>> calculation were done ( the name_of_my_job.log file was empty and no
>>> update
>>> of .trr file was seen ). Commonly this error occurs when I uses many
>>> nodes
>>> (8-10) Finally sometimes I've obtain some errors with the PME order (
>>> this
>>> time I've used 3 nodes). The exactly error differs when I varry the
>>> number
>>> of nodes.
>>>
>>>
>>> Could you tell me whats wrong could be with my cluster?
>>>
>>> Thanks for help
>>>
>>> James
>>>
>>
>>
>

Re: [gmx-users] Generation of the Distance Restraints

[James Starlight]

> 2) Also I've found that there is more simple way to define restraines
> based on the BONDS enty in the topology file. Could you provide me with the
> more information about this simpler way ?
>
>
> Simpler, but not a restraint to within a region. The manual section we are
> discussing links you to the available documentation elsewhere in the
> manual. I don't have the time to help with every interpretation question
> you might have.
>
> Mark
>
> Mark,


In more details I want to generate network of disres for all helices
H-bonds. So I want to restraint H-bond distance between i and i+4 atoms of
the backbone.

What is the simplest way to do such task? I think that the ussage of
genrestr -disre could be useful for such generation of the complex disres
because of the size of my protein. But how I could define the restrained
atoms (i, i+4 atoms ) ? In the make_ndx options I didnt find the most
trivial sollution of the such choise. So the only sollution is to define
each I and I+4 atoms of the backbone manualy, isnt it ?

James
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Re: [gmx-users] Problems with simulation on multi-nodes cluster

[James Starlight]

Could someone tell me what tell the below error

Getting Loaded...
Reading file MD_100.tpr, VERSION 4.5.4 (single precision)
Loaded with Money


Will use 30 particle-particle and 18 PME only nodes
This is a guess, check the performance at the end of the log file
[ib02:22825] *** Process received signal ***
[ib02:22825] Signal: Segmentation fault (11)
[ib02:22825] Signal code: Address not mapped (1)
[ib02:22825] Failing at address: 0x10
[ib02:22825] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xf030)
[0x7f535903e03$
[ib02:22825] [ 1] /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x7e23)
[0x7f535$
[ib02:22825] [ 2] /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x8601)
[0x7f535$
[ib02:22825] [ 3] /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x8bab)
[0x7f535$
[ib02:22825] [ 4] /usr/lib/openmpi/lib/openmpi/mca_btl_sm.so(+0x42af)
[0x7f5353$
[ib02:22825] [ 5] /usr/lib/libopen-pal.so.0(opal_progress+0x5b)
[0x7f535790506b]
[ib02:22825] [ 6] /usr/lib/libmpi.so.0(+0x37755) [0x7f5359282755]
[ib02:22825] [ 7] /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so(+0x1c3a)
[0x7f$
[ib02:22825] [ 8] /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so(+0x7fae)
[0x7f$
[ib02:22825] [ 9] /usr/lib/libmpi.so.0(ompi_comm_split+0xbf)
[0x7f535926de8f]
[ib02:22825] [10] /usr/lib/libmpi.so.0(MPI_Comm_split+0xdb) [0x7f535929dc2b]
[ib02:22825] [11]
/usr/lib/libgmx_mpi_d.openmpi.so.6(gmx_setup_nodecomm+0x19b) $
[ib02:22825] [12] mdrun_mpi_d.openmpi(mdrunner+0x46a) [0x40be7a]
[ib02:22825] [13] mdrun_mpi_d.openmpi(main+0x1256) [0x407206]
[ib02:22825] [14] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd)
[0x7f$
[ib02:22825] [15] mdrun_mpi_d.openmpi() [0x407479]
[ib02:22825] *** End of error message ***
--
mpiexec noticed that process rank 36 with PID 22825 on node ib02 exited on
sign$
--


I've obtained it when I've tried to use my system on multi-node station (
there is no problem on single node). Does this problem with the cluster
system or something wrong with parameters of my simulation?


JAmes

15 марта 2012 г. 15:25 пользователь James Starlight
написал:

> Mark, Peter,
>
>
> I've tried to do .tpr file on my local CPU and launch only
>
> mpiexec -np 24 mdrun_mpi_d.openmpi -v -deffnm MD_100
>
> on the cluster with 2 nodes.
>
> I see my job as working but when I've checking the MD_100.log (attached)
> file there are no any information about simulation steps in that file (
> when I use just one node I see in that file step-by-step progression of my
> simulation like below wich was find in the same log file for ONE NODE
> simulation ):
>
> Started mdrun on node 0 Thu Mar 15 11:22:35 2012
>
>Step   Time Lambda
>   00.00.0
>
> Grid: 12 x 9 x 12 cells
>Energies (kJ/mol)
>G96AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
> 1.32179e+043.27485e+032.53267e+034.06443e+026.15315e+04
> LJ (SR)LJ (LR)  Disper. corr.   Coulomb (SR)   Coul. recip.
> 4.12152e+04   -5.51788e+03   -1.70930e+03   -4.54886e+05   -1.46292e+05
>  Dis. Rest. D.R.Viol. (nm) Dih. Rest.  PotentialKinetic En.
> 2.14240e-023.46794e+001.33793e+03   -4.84889e+059.88771e+04
>Total Energy  Conserved En.Temperature Pres. DC (bar) Pressure (bar)
>-3.86012e+05   -3.86012e+053.11520e+02   -1.14114e+023.67861e+02
>Constr. rmsd
> 3.75854e-05
>
>Step   Time Lambda
>20004.00.0
>
>Energies (kJ/mol)
>G96AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
> 1.31741e+043.25280e+032.58442e+033.51371e+026.15913e+04
> LJ (SR)LJ (LR)  Disper. corr.   Coulomb (SR)   Coul. recip.
> 4.16349e+04   -5.53474e+03   -1.70930e+03   -4.56561e+05   -1.46485e+05
>  Dis. Rest. D.R.Viol. (nm) Dih. Rest.  PotentialKinetic En.
> 4.78276e+013.38844e+009.82735e+00   -4.87644e+059.83280e+04
>Total Energy  Conserved En.Temperature Pres. DC (bar) Pressure (bar)
>-3.89316e+05   -3.87063e+053.09790e+02   -1.14114e+027.25905e+02
>Constr. rmsd
> 1.88008e-05
>
> end etc...
>
>
>
> What's wrong can be with multi-node computations?
>
>
> James
>
>
> 15 марта 2012 г. 11:25 пользователь Mark Abraham 
> написал:
>
> On 15/03/2012 6:13 PM, Peter C. Lai wrote:
>>
>>> Try separating your grompp run from your mpirun:
>>> You should not really be having the scheduler execute the grompp. Run
>>> your grompp step to generate a .tpr either on the head node or on your
>>> loca

Re: [gmx-users] Generation of the Distance Restraints

[James Starlight]

This days I tested some distance restrains applied on my protein. I had
some literature data  from wich I've used such restrains as well as similar
wirk where authors applied this data on the same protein to view some
biological-relevant event :)

I've applied my restrains gradually to rise force from 0.1 to 30 kj nm mol
in mdp file.

During such task I've noticed some disagreements between distances wich I
obtained after simulation as well as experimetnal data

E.g in the topology file I've defined 2 restrains

  1258 2203 115 1 0.450 0.650 1.600 1.0

  1255 2742 116 1 1.900 2.150 3.150 1.0

In this case this means that I defined first restrains betwenn 0.45 0.650) and betwen the second pair
of atoms 1.5 ( less than lowest R0 threshold 1.9 ).

Why such disagreements have been occured ? Should I define restrains range
more accurately ? (e.g if I want to restrain atoms in the distance equal to
0.5 nm so such harmonic restrains should be 0.45 0.55 for r0 and r1
respectyally. )


Thanks for help,


James
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[gmx-users] Principal Components Analysis in Gromacs

[James Starlight]

Dear Gromacs Users!



I have some questions about PCA implemented in Gromacs.


1- I want to increase amplitude of the motions seen on the selected PCs but
I can't found scalling factor option for that.


2- I have calculated MD trajectory for my protein. From this trajectory I
want to find some relevant motions by means of PCA analysis. Also I have
dataset of the experimental structures of that protein where this motion
also presents ( e.g active and innactive conformations of my protein
included in my dataset) As the consequence I want to compare overal
direction of the motion observed along some PCs calculated from MD
trajectory ( it's called EDA) with the motion observed olong other PCs wich
was calculated from the enssemble of the pdb structures. As I've noticed
via  g_anaeig I can compare such datasets by means of -v and -v2 flaggs.
For this purpose I must make trajectory for my X-ray structures at first
and load it with the MD trajectory into the g_anaeig -v md.trr -v2
x_ray.trr. Would this aproach be correct in general ? What should I do if
both of my datasets consist of different number of backbone atoms (due to
some missing residues in the X-ray data) ?


Thanks for help,


James
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Re: [gmx-users] Generation of the Distance Restraints

[James Starlight]

Mark,

This sounds like I use very small forces but expect reasonable effect. But
I've applied different forces with step-by-step increasing of force
constants ( from very softest comparable with the thermal motion ( 0.1 kj
mol nm-2) to relatively hight (10).  As the consequence I've observed
effect of application of that harmonic constraints wich I've defined in the
r0 and r1 range but in some case ( where forses were were hight I've seen
perturbation of my structures) and when constraints were low ( in
accordance to my literature) I've not seen desired effect like the
selection of the constraints was wrong ( but actually all restraints were
applied on the correct possitions). This was seen by measurement of the
distances between atom pairs wich were contrained. Eg If I define this
distances in the 0.1написал:

> If there's a car at the bottom of one valley in the Alps, and you think it
> should be two valleys over, and you pull it with a trained cat... it's not
> going to move much. How big an animal you need depends on the geography.
> There need not even be a reasonable route for you to take, if the target
> valley is effectively on Mars.
>
> Mark
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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Re: [gmx-users] Principal Components Analysis in Gromacs

[James Starlight]

Hi Tsjerk!

First, I'd like also thanks you for your  help.


Today I tried to make PCA of my X-ray data as well as comparison between
results of such PCA and EDA ( PCA wich is based on the MD trajectory of the
same protein).

In generaly I have no any problems with the X-ray PCA but I've forced with
some during comparison of results of both PCAs due to the different atom
numbers in both datasets ( X-ray structures consist of missing atoms ). As
I understood this problem could be solved by selection atoms for the MD
trajectory ( before PCA calculation of that data) wich are present in all
X-ray structures.

Because of the X-ray dataset consist of some missing residues in the loops
of structures I've had to reduce atom numbers in initial tpr topology.
So by means of tpbconv  I've made new .tpr file for this X-ray structures.
This new TPR was based on the  .tpr file wich I've obtained from the MD of
full-atomic model of protein. In new TPR I include only mainchain atoms as
well as residues presented in the X-ray structures ( I've defined it by
means of index.ndx file ). Does this aproach correct ? Are there any extra
ways to obtaint TPR file for my X-ray dataset  without redusing topology of
the MD structure ?

Also I'd like to ask some more about PCA results.

1) Firstly, what exactly is the new compresed trajectory made by
-filt filtered.xtc

In case of x-ray PCA this trajectory correspond to the initial numbers of
pdb's files but in case of MD_based PCA this trajectory consist of redused
number of atoms.

2) Also I'd like to know what actyally is the
-extr extremePCA.pdb ?

In case of MD_based PCA I've obtaned 20 different extreme.pdb trajectories
where 20 was the number of calculated Principal components.

But in case of X-ray PCA I've obtained only one such file wich was similar
to visualisation of the motion along softest PC althrough I've calculated
10 eigenvectors. Why in case of PCA I've obtain only one such file and what
exactly this trajectory is ? Is there any extra methods to visualise
motions along specified components ( not for ensembles of components )?

3) How I could specify exactly number of PC in the projection graphs ? AS I
understood 2d and 3d projections are made along the -first and -last
components. How I can make such projections based on two/ three another
specified components (e.g along 2 and 7 modes from 20 calculated) ?


Thanks for help,


James




28 марта 2012 г. 18:02 пользователь Tsjerk Wassenaar написал:

> Hi Thomas,
>
> > Thanks for all the clarifications about PCA you make on the mailing list!
>
> Thank you for the appreciation :)
>
> > I have a question about the commandlines you wrote. Why do you use the
> .tpr
> > file with the "-s" flag? Is it because you want to compare the
> > mass-wheighted covariance matrices? I use to calculate the covariance
> > matrices by giving to g_covar a .pdb file with the "-s" flag and then
> > calculate the RMSIP without giving any structure file. I guess no masses
> are
> > used in that covariance analysis, right? Do you recommend using atom
> masses
> > for PCA in general?
>
> Well, I admit that in most cases I don't use mass-weighting myself.
> Unless you include hydrogens, it also doesn't matter much, as the
> masses are not very different. Only if you want to calculate
> frequencies, e.g. to connect to NMA and/or IR spectroscopy you would
> really need masses.
> If you use a .pdb or .gro file, you don't get mass-weighting. And
> you're right that for calculating the RMSIP, and the subspace overlap,
> and the martix of inner products, you don't need a structure filel,
> but only the eigenvectors, and possibly the eigenvalues.
>
> Cheers,
>
> Tsjerk
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Generation of the Distance Restraints

[James Starlight]

Mark,


thanks for explanation again.


28 марта 2012 г. 16:04 пользователь Mark Abraham
написал:

 That can mean big restraint forces and tiny integration steps and lots of
> tweaking and praying.
>

Yes I think this aproach could be usefull in my case. Actually I want to
move some parts of the helices of my protein in the deired direction up to
6-10 A. There is the data showing that this new conformation is very
unstabile and short-lived in the absense of some additional external
factors. But also I've seen that application of big restrained forces
perturbed the overal structure of my protein considerably. So the good
sollution might be application of such forces  with the position restraines
simultaneously. What do you think about the most trivial aproach: e.g if I
could not applied posres on the desired atoms and use default posres
generated by pdb2gmx on the all atoms. At the same time I'm using more
strongest distance restrains on the desired positions to move this atoms
even the precense of weaker posres applied on this. Finally because posres
act on the others atoms I can prevent destabilisation of the whole protein.
Might this aproach be usefull? And what difference between forses of the
posres ( 1000 kj) and disres must be to generate expected effect ?


James

>
>
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[gmx-users] Editing of the existing system

[James Starlight]

Dear Gromacs Users!


I have some system wich consist of protein in membrane-mimicking layer
surrounded by water. I want to modify my existing system by adding small
peptide fragment to this system. I want to dock this peptide to the some
part of my protein wich is situated  in the bottom water layer.

While doing such task I've aligned both of the components of new system in
one desired dimmension so as the consequence I have peptide.gro file in the
desired orientation relative to my system.

Now as I understood there are 2 possible ways

1- Manually copy_past peptide.gro into the system and run minimisation.

2- More accuracy- using genbox for such task

genbox -cp Gs.gro -cs system.gro -o new.gro

where Gs.gro is my peptide and system.gro is the system.

But when I've tried such task I've obtain only peptide as well as some
solvent ( small part of water) as the consequence. How I could fix it to
obtain desired system with the removed overlapping water with the new
peptide ? What are the additions tips could you provide me about such
docking ?

Thanks,

JAmes
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Re: [gmx-users] Editing of the existing system

[James Starlight]

Mark,


Also I'd like to know some more about most correct parametrisation of such
new edited system. My new system consist of two proteins ( one- wich was
initially and the second small peptide wich I've docked to the first
protein). So now I need to define 2 separate groups for the below enties of
my MD files

energygrps = Protein peptide

tc-grps = Protein_Bilayer SOL_ions_peptide

and finally CoM groups because of the general anisotropy of the membrane system

comm-grps   = Protein_Bilayer SOL_Ions_Peptide

I've made itp file for the peptide via pdb2gmx so in th default
definition both the protein and peptide are the protein enty in the
index file.

I've separate both of the protein and peptide by selection of two
subsets of atoms wich represent to the each of that enties.

So finally I have two groups in the index.ndx file

a_1-5000  ( it's protein)
a_-10500 (it's peptide)

Does this separation correct in general ? I have some fears because
both protein and peptide consist of the same residue numbers in the
GRO file ( e.g there are 212- lys wich is part of the protein and
212-Pro wich is part of the peptide ) Might this system be tended to
errors?
I have no errors during processing of that sustem by grompp as well as
md run. What should I do for such system consisted of two proteins in
separate phases ( membrane-like and water)
?

Thanks for help again,

James




30 марта 2012 г. 17:34 пользователь Mark Abraham
написал:

> Constructing a system is normally easiest if you remove all your
> solvent(s), paste in your interesting molecules somehow or other, and then
> rebuild the solvent with tools like genbox.
>
> Mark
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Re: [gmx-users] Editing of the existing system

[James Starlight]

Mark,


I've forced with some problems during MDrun of such system with the two
proteins.

Firstly, after addition of second protein, I've removed all water and ions
and solvated my system with genbox and genion.

Than I've redefined groups of my proteins ( wich are like a_1-4000 and
a_4001-5000 ) in index.ndx file in the separate T_coupl, COM and
energygroups because atom order was perturbed after solvation.

Than I've minimized my system  with the Emtool=500

The problems were on the nvt equilibration phase with the posres applied on
the both proteins. I have no errors, notes or warninngs from GROMPP but
when I've started my simulation with MDrun my system was crushed on the 1st
step with the multiple LINKS warnings as well as message that something
wrong with interactions between 1st protein atoms and surrounded water ( as
I've said previously after addition of the second protein to my system I've
resolvated my system again).

Might my system be not properly minimized  or does something wrong else in
addition?


James

31 марта 2012 г. 2:20 пользователь Mark Abraham
написал:

>  On 31/03/2012 1:00 AM, James Starlight wrote:
>
> Mark,
>
>
> Also I'd like to know some more about most correct parametrisation of such
> new edited system. My new system consist of two proteins ( one- wich was
> initially and the second small peptide wich I've docked to the first
> protein). So now I need to define 2 separate groups for the below enties of
> my MD files
>
> energygrps = Protein peptide
>
> tc-grps = Protein_Bilayer SOL_ions_peptide
>
> and finally CoM groups because of the general anisotropy of the membrane 
> system
>
>
> comm-grps = Protein_Bilayer SOL_Ions_Peptide
>
> I've made itp file for the peptide via pdb2gmx so in th default definition 
> both the protein and peptide are the protein enty in the index file.
>
> I've separate both of the protein and peptide by selection of two subsets of 
> atoms wich represent to the each of that enties.
>
>
> So finally I have two groups in the index.ndx file
>
> a_1-5000  ( it's protein)
> a_-10500 (it's peptide)
>
>
> You can use make_ndx (or a text editor on the .ndx file) to give them more
> helpful names.
>
>
>  Does this separation correct in general ? I have some fears because both 
> protein and peptide consist of the same residue numbers in the GRO file ( e.g 
> there are 212- lys wich is part of the protein and 212-Pro wich is part of 
> the peptide ) Might this system be tended to errors?
>
>
> Residue numbers are largely irrelevant. pdb2gmx and maybe grompp use them
> for matching a coordinate file to the .rtp and .top (respectively), but
> only really in the sense that the number changes from one residue to
> another.
>
>
>  I have no errors during processing of that sustem by grompp as well as md 
> run. What should I do for such system consisted of two proteins in separate 
> phases ( membrane-like and water)
> ?
>
>
> All seems basically sound.
>
> Mark
>
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Re: [gmx-users] Editing of the existing system

[James Starlight]

Justin,

I've minimised my system to emtool=1.0
but the error still occurs


31 марта 2012 г. 16:27 пользователь Justin A. Lemkul написал:

>
> Separate COM motion removal groups are tricky.  I'm still not completely
> clear on what your system looks like, but if you've got two proteins in two
> layers of solvent and you expect one or both of them to move in such a way
> that they begin to interact, it may not be appropriate to be using the
> groups you've shown below.


 My system consist of membrane receptor in membrane-like bilayer surrounded
by water. Also part of the receptor is in the water layer. To this part
wich are in the water another water-soluble protein ( part of the
G-protein) has been attached.



> And what was the exact outcome?


This is the error log

Getting Loaded...
Reading file nvt.tpr, VERSION 4.5.4 (single precision)
Loaded with Money


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002373, max 0.102422 (between atoms 1387 and 1388)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
starting mdrun 'B2ar_in_Ccl4 in water'
50 steps,   1000.0 ps.

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 73.552702, max 3051.386475 (between atoms 8551 and 8552)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1407   1412   34.80.1530   0.1955  0.1530
   1407   1408   35.20.1530   0.1943  0.1530
   1405   1407  152.50.1471   0.1638  0.1470
   1405   1406  123.60.1001   0.2394  0.1000
etc - the above- part of atoms of the first protein


   8519   8520   44.30.1001   0.1498  0.1000
   8517   8519   41.60.1331   0.1901  0.1330
   8478   8480   54.90.1330   0.1555  0.1330
   8478   8479   44.80.1230   0.1262  0.1230
   8465   8478   52.70.1530   0.1491  0.1530
this is part of atoms of the second protein


Also I've attached my nvt.mdp file

in this file
 a_1-4232 is the first protein
 a_8365-8643 is the second protein.


What's wrong with this system?

James


nvt.mdp
Description: Binary data
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Re: [gmx-users] Editing of the existing system

[James Starlight]

Justin,

31 марта 2012 г. 18:18 пользователь Justin A. Lemkul написал:

>
> Start by inspecting the initial configuration in the vicinity of these
> atoms. Something is likely clashing here.


Yes, I've checked both of the proteins and found that the problem atoms
were situated exactly in the docked region of the both proteins. So It
seems that there are some clashes between atoms in the docked site. By the
way this site of the first protein ( Receptor) consist of 2 flexible loops
and the rigid helix from the second protein. ( fragment of G-protein) Might
the energy minimisation solve this problem generally ? ( e.g by means of CG
minimisation to very low forces aplied on atoms). Is there any possible
ways to change conformation of the flexible loops during minimisation\
equilibration phases without aplication of any external forces?

James
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Re: [gmx-users] Editing of the existing system

[James Starlight]

Justin,

Sorry that I can't provide you with such information now because that data
have been left in my lab workstation. Tomorrow I'll find all this logs and
attach it to this topic. Also I've run more properly CG minimisation (
EMtool=0.01) in double precission mode. I'll check this results too and
attach all logs here.


Many thanks again for help

James

31 марта 2012 г. 21:57 пользователь Justin A. Lemkul написал:

>
>
> James Starlight wrote:
>
>> Justin,
>>
>> 31 марта 2012 г. 18:18 пользователь Justin A. Lemkul > jalem...@vt.edu>> написал:
>>
>>
>>
>>Start by inspecting the initial configuration in the vicinity of
>>these atoms. Something is likely clashing here.
>>
>>
>> Yes, I've checked both of the proteins and found that the problem atoms
>> were situated exactly in the docked region of the both proteins. So It
>> seems that there are some clashes between atoms in the docked site. By the
>> way this site of the first protein ( Receptor) consist of 2 flexible loops
>> and the rigid helix from the second protein. ( fragment of G-protein) Might
>> the energy minimisation solve this problem generally ? ( e.g by means of CG
>> minimisation to very low forces aplied on atoms). Is there any possible
>> ways to change conformation of the flexible loops during minimisation\
>> equilibration phases without aplication of any external forces?
>>
>>
> Proper EM should resolve such clashes, but under normal circumstances that
> should have happened already.  You may have to do EM in vacuo before adding
> any solvent to allow for proper resolution of clashes.  I'm only guessing
> at this point.  I have asked twice for the output of your previous EM
> attempts, which would give me a much better idea of where things stand.
>  Since you haven't answered those questions, I'll leave it up to you to try
> to resolve.  Good luck.
>
> -Justin
>
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
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Fwd: [gmx-users] Editing of the existing system

[James Starlight]

Justin,

Sorry again for the delay.

I've finished minimise my system with the CG algorithm in double precision
( after steep minimisation )
but the output was

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 0.1

Than I've tried to equilibrate this system with the NVT conditions and
obtain old error about collapse of my system :)

 I've found logs of both minimisation ( both of the logs  were very big
I've coppied only end part of those output data )  and attach it to this
topic.

Also I've run minimisation in vacuum as you've told me but this results
would be aviable tomorrow.

Could you tell me whats exactly wrong with that system and is there
possible ways to fix the problem?

Thanks for help


James

31 марта 2012 г. 22:05 пользователь James Starlight
написал:

Justin,
>
> Sorry that I can't provide you with such information now because that data
> have been left in my lab workstation. Tomorrow I'll find all this logs and
> attach it to this topic. Also I've run more properly CG minimisation (
> EMtool=0.01) in double precission mode. I'll check this results too and
> attach all logs here.
>
>
> Many thanks again for help
>
> James
>
> 31 марта 2012 г. 21:57 пользователь Justin A. Lemkul написал:
>
>
>>
>> James Starlight wrote:
>>
>>> Justin,
>>>
>>> 31 марта 2012 г. 18:18 пользователь Justin A. Lemkul 
>>> >> jalem...@vt.edu>> написал:
>>>
>>>
>>>
>>>Start by inspecting the initial configuration in the vicinity of
>>>these atoms. Something is likely clashing here.
>>>
>>>
>>> Yes, I've checked both of the proteins and found that the problem atoms
>>> were situated exactly in the docked region of the both proteins. So It
>>> seems that there are some clashes between atoms in the docked site. By the
>>> way this site of the first protein ( Receptor) consist of 2 flexible loops
>>> and the rigid helix from the second protein. ( fragment of G-protein) Might
>>> the energy minimisation solve this problem generally ? ( e.g by means of CG
>>> minimisation to very low forces aplied on atoms). Is there any possible
>>> ways to change conformation of the flexible loops during minimisation\
>>> equilibration phases without aplication of any external forces?
>>>
>>>
>> Proper EM should resolve such clashes, but under normal circumstances
>> that should have happened already.  You may have to do EM in vacuo before
>> adding any solvent to allow for proper resolution of clashes.  I'm only
>> guessing at this point.  I have asked twice for the output of your previous
>> EM attempts, which would give me a much better idea of where things stand.
>>  Since you haven't answered those questions, I'll leave it up to you to try
>> to resolve.  Good luck.
>>
>> -Justin
>>
>>
>> --
>> ==**==
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==**==
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> Please search the archive at http://www.gromacs.org/**
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>>  posting!
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>>
>
>
   Energies (kJ/mol)
   BondG96Bond  Angle   G96AngleProper Dih.
2.17169e+011.57043e+041.18166e+013.08747e+032.44110e+03
  Improper Dih.  LJ-14 Coulomb-14LJ (SR)LJ (LR)
1.06376e+03   -5.54923e+026.27182e+045.82867e+04   -5.68584e+03
   Coulomb (SR)   Coul. recip.  Potential Pressure (bar)
   -5.44409e+05   -1.65023e+05   -5.72338e+05   -1.71569e+04

   Step   Time Lambda
  1197311973.00.0

   Step   Time Lambda
  1197411974

Re: [gmx-users] Editing of the existing system

[James Starlight]

Justin,

Thanks again for attention to my problem.


I've checked my system and found that the problem was exactly in the 1388
atom ( wich is not properly minimized in accordance to the log files). This
atom is the Cb atom of Gln residue wich placed between one loop of the
protein and docked alpha helix of the peptide. The  surrounding of that
atom ( It's likely that other intracellular loops of the receptor as well
as long N term protect this side chain to rotate during the minimisation ).
When I've checked pdb files produced by exploding system I've found that
some atoms ( from that loops) were moved from the pereodic boundaries (
I've obtain very big system as the conseqyence surrounding by some single
atoms. So it all look like as big artifact :) )

So it seems that I need to use slightly different initial conformation of
the receptor because minimisation could not to resolve such crushes.


Thanks again


James

1 апреля 2012 г. 21:37 пользователь Justin A. Lemkul написал:

>
>
> James Starlight wrote:
>
>> Justin,
>>
>> Sorry again for the delay.
>>
>> I've finished minimise my system with the CG algorithm in double
>> precision ( after steep minimisation )
>> but the output was
>>
>> Stepsize too small, or no change in energy.
>> Converged to machine precision,
>> but not to the requested precision Fmax < 0.1
>>
>> Than I've tried to equilibrate this system with the NVT conditions and
>> obtain old error about collapse of my system :)
>>
>>  I've found logs of both minimisation ( the step minimisation log was
>> very big I've coppied only end part of this output data )  and attach it to
>> this topic.
>>
>>
> Both of these log files indicate that EM was likely fine.  For future
> reference, the following sections were all I was asking for all along:
>
> From CG:
> Potential Energy  = -5.96597537065782e+05
> Maximum force =  1.42815783701700e+02 on atom 1388
> Norm of force =  1.58963638409829e+00
>
> From steep:
> Potential Energy  = -5.7233788e+05
> Maximum force =  7.0209003e+02 on atom 1388
> Norm of force =  1.1310696e+01
>
> CG gives you the better minimization, overall, as expected.  Atom 1388
> bears the maximum force, but it is not of problematic magnitude.
>
>
>  Also I've run minimisation in vacuum as you've told me but this results
>> would be aviable tomorrow.
>>
>>
> It's probably not necessary, after all.  I was guessing at that point
> based on incomplete information.
>
>
>  Could you tell me whats exactly wrong with that system and is there
>> possible ways to fix the problem?
>>
>>
> As I've said before, the only strange thing you seem to be doing is with
> your comm-grps.  Change this setting to "System" and see if it runs.
>  Otherwise, I can find no reason for the immediate instability.  If it
> still crashes, perhaps decrease the time step for the initial equilibration.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
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Re: [gmx-users] Problems with simulation on multi-nodes cluster

[James Starlight]

Mark,

As I've told previously I have problems with the running simulation in
multi-node mode.

I checked logs of such simulations and fond like this

Will use 10 particle-particle and 6 PME only nodes
This is a guess, check the performance at the end of the log file
Using 6 separate PME nodes

This simulation was run on the 2 nodes ( 2*8 CPUs). And I've never obtain
the same notions about PME nodes when I've launch my systems on the singe
node. Might it be that some special options for the PME nodes are needed in
the mdp file to be defined ?

James

20 марта 2012 г. 18:02 пользователь Mark Abraham
написал:

> On 20/03/2012 10:35 PM, James Starlight wrote:
>
>> Could someone tell me what tell the below error
>>
>> Getting Loaded...
>> Reading file MD_100.tpr, VERSION 4.5.4 (single precision)
>> Loaded with Money
>>
>>
>> Will use 30 particle-particle and 18 PME only nodes
>> This is a guess, check the performance at the end of the log file
>> [ib02:22825] *** Process received signal ***
>> [ib02:22825] Signal: Segmentation fault (11)
>> [ib02:22825] Signal code: Address not mapped (1)
>> [ib02:22825] Failing at address: 0x10
>> [ib02:22825] [ 0] /lib/x86_64-linux-gnu/**libpthread.so.0(+0xf030)
>> [0x7f535903e03$
>> [ib02:22825] [ 1] /usr/lib/openmpi/lib/openmpi/**mca_pml_ob1.so(+0x7e23)
>> [0x7f535$
>> [ib02:22825] [ 2] /usr/lib/openmpi/lib/openmpi/**mca_pml_ob1.so(+0x8601)
>> [0x7f535$
>> [ib02:22825] [ 3] /usr/lib/openmpi/lib/openmpi/**mca_pml_ob1.so(+0x8bab)
>> [0x7f535$
>> [ib02:22825] [ 4] /usr/lib/openmpi/lib/openmpi/**mca_btl_sm.so(+0x42af)
>> [0x7f5353$
>> [ib02:22825] [ 5] /usr/lib/libopen-pal.so.0(**opal_progress+0x5b)
>> [0x7f535790506b]
>> [ib02:22825] [ 6] /usr/lib/libmpi.so.0(+0x37755) [0x7f5359282755]
>> [ib02:22825] [ 7] /usr/lib/openmpi/lib/openmpi/**mca_coll_tuned.so(+0x1c3a)
>> [0x7f$
>> [ib02:22825] [ 8] /usr/lib/openmpi/lib/openmpi/**mca_coll_tuned.so(+0x7fae)
>> [0x7f$
>> [ib02:22825] [ 9] /usr/lib/libmpi.so.0(ompi_**comm_split+0xbf)
>> [0x7f535926de8f]
>> [ib02:22825] [10] /usr/lib/libmpi.so.0(MPI_Comm_**split+0xdb)
>> [0x7f535929dc2b]
>> [ib02:22825] [11] 
>> /usr/lib/libgmx_mpi_d.openmpi.**so.6(gmx_setup_nodecomm+0x19b)
>> $
>> [ib02:22825] [12] mdrun_mpi_d.openmpi(mdrunner+**0x46a) [0x40be7a]
>> [ib02:22825] [13] mdrun_mpi_d.openmpi(main+**0x1256) [0x407206]
>> [ib02:22825] [14] /lib/x86_64-linux-gnu/libc.so.**6(__libc_start_main+0xfd)
>> [0x7f$
>> [ib02:22825] [15] mdrun_mpi_d.openmpi() [0x407479]
>> [ib02:22825] *** End of error message ***
>> --**--**
>> --
>> mpiexec noticed that process rank 36 with PID 22825 on node ib02 exited
>> on sign$
>> --**--**
>> --
>>
>>
>> I've obtained it when I've tried to use my system on multi-node station (
>> there is no problem on single node). Does this problem with the cluster
>> system or something wrong with parameters of my simulation?
>>
>
> The trace back suggests your MPI system is not configured correctly for
> your hardware.
>
> Mark
>
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Re: [gmx-users] Editing of the existing system

[James Starlight]

By the way

Today I've examined in vacuum minimisation outputs more carefully (
watching in vmd trr ) and found that conformation of the loops in the
docked regions were changed after long CG minimisation.

Then I've resolvate my system and add ions and run STEEP minimisation of
that system.

After this I've decreasing integration step to the from 0.001 to 0.0001.

Unfortunatelly the error was the same

starting with the LINK warnings like

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002089, max 0.082711 (between atoms 1387 and 1388)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length


and ending with the exploiding of my system as well with the eror like

step 29: Water molecule starting at atom 42310 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates


Also I've changed COM groups ( to the System value in one case as well as
placing the second protein group to the common group with the first protein
and membrane in the second case ). But the result was the same.


Is there any  suggestions or should I start with another conformation of
first protein ?


James



2 апреля 2012 г. 9:56 пользователь James Starlight
написал:

> Justin,
>
> Thanks again for attention to my problem.
>
>
> I've checked my system and found that the problem was exactly in the 1388
> atom ( wich is not properly minimized in accordance to the log files). This
> atom is the Cb atom of Gln residue wich placed between one loop of the
> protein and docked alpha helix of the peptide. The  surrounding of that
> atom ( It's likely that other intracellular loops of the receptor as well
> as long N term protect this side chain to rotate during the minimisation ).
> When I've checked pdb files produced by exploding system I've found that
> some atoms ( from that loops) were moved from the pereodic boundaries (
> I've obtain very big system as the conseqyence surrounding by some single
> atoms. So it all look like as big artifact :) )
>
> So it seems that I need to use slightly different initial conformation of
> the receptor because minimisation could not to resolve such crushes.
>
>
> Thanks again
>
>
> James
>
> 1 апреля 2012 г. 21:37 пользователь Justin A. Lemkul написал:
>
>
>>
>> James Starlight wrote:
>>
>>> Justin,
>>>
>>> Sorry again for the delay.
>>>
>>> I've finished minimise my system with the CG algorithm in double
>>> precision ( after steep minimisation )
>>> but the output was
>>>
>>> Stepsize too small, or no change in energy.
>>> Converged to machine precision,
>>> but not to the requested precision Fmax < 0.1
>>>
>>> Than I've tried to equilibrate this system with the NVT conditions and
>>> obtain old error about collapse of my system :)
>>>
>>>  I've found logs of both minimisation ( the step minimisation log was
>>> very big I've coppied only end part of this output data )  and attach it to
>>> this topic.
>>>
>>>
>> Both of these log files indicate that EM was likely fine.  For future
>> reference, the following sections were all I was asking for all along:
>>
>> From CG:
>> Potential Energy  = -5.96597537065782e+05
>> Maximum force =  1.42815783701700e+02 on atom 1388
>> Norm of force =  1.58963638409829e+00
>>
>> From steep:
>> Potential Energy  = -5.7233788e+05
>> Maximum force =  7.0209003e+02 on atom 1388
>> Norm of force =  1.1310696e+01
>>
>> CG gives you the better minimization, overall, as expected.  Atom 1388
>> bears the maximum force, but it is not of problematic magnitude.
>>
>>
>>  Also I've run minimisation in vacuum as you've told me but this results
>>> would be aviable tomorrow.
>>>
>>>
>> It's probably not necessary, after all.  I was guessing at that point
>> based on incomplete information.
>>
>>
>>  Could you tell me whats exactly wrong with that system and is there
>>> possible ways to fix the problem?
>>>
>>>
>> As I've said before, the only strange thing you seem to be doing is with
>> your comm-grps.  Change this setting to "System" and see if it runs.
>>  Otherwise, I can find no reason for the immediate instability.  If it
>> still crashes, perhaps decrease the time step for the initial equilibration.
>>
>>
>> -Justin
>>
>> --
>> ==**

[gmx-users] Simulation in the high temperature conditions

[James Starlight]

Dear Gromacs users!


I want to perform simulation of the membrane protein in the
Ccl4-membrane-mimicking interiour in the increaced ( up to 600 K)
temperature on the nvt ensemble.

As the consequence I'd like to protect the temperature caused
destabilisation of my protein and simulate native-like conformation events
in the speed-up manner.

What should I use for preparing of my system? As I understtod I neen long
nvt equilibration phase prior to productive run to addaptate my system to
the uncommon conditions. For this I want to perform step-by-step increasing
of the Ref_T for all separate groups of my system ( Protein_Ccl4,
Water_Ions ). E.g I'll separate my equilibration phase on the 20 steps with
the ref_t 310, 320, 330... 600K and the length of each step 50ps. Could
this aproach could be usefull? What addition tricks could I use ( e.g
dynamics of changing tau_t for different groups etc)?


Thanks for help,


James
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[gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

So if it were not quite clearly :)

 my main question is about methodology of such gradually temperature rise
in the nvt enssemble conditions. Might it be realised by means of simple
equilibation in one mdp file varying some parametries to change time-step
of temperature growth? Or this methodology require several mdp files with
slightly different ref_t as well as gen_temp options ? Finally what exactly
is tau_t time constant?

James

3 апреля 2012 г. 13:14 пользователь James Starlight
написал:

> Dear Gromacs users!
>
>
> I want to perform simulation of the membrane protein in the
> Ccl4-membrane-mimicking interiour in the increaced ( up to 600 K)
> temperature on the nvt ensemble.
>
> As the consequence I'd like to protect the temperature caused
> destabilisation of my protein and simulate native-like conformation events
> in the speed-up manner.
>
> What should I use for preparing of my system? As I understtod I neen long
> nvt equilibration phase prior to productive run to addaptate my system to
> the uncommon conditions. For this I want to perform step-by-step increasing
> of the Ref_T for all separate groups of my system ( Protein_Ccl4,
> Water_Ions ). E.g I'll separate my equilibration phase on the 20 steps with
> the ref_t 310, 320, 330... 600K and the length of each step 50ps. Could
> this aproach could be usefull? What addition tricks could I use ( e.g
> dynamics of changing tau_t for different groups etc)?
>
>
> Thanks for help,
>
>
> James
>
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Re: [gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

Justin,thanks!


1) For example for the situation presented in manual for 2 groups with 3
and 4 points the time enty should be

annealing_time = 0 3 6 0 2 4 6

from this I've understood that 0 value is the start of timer for each group
and subsequent values are the actual time in the ps, havennt it ?

For example I'd like to perform nvt simulation ( with overal time 100ps)
for three different groups in 5 equal steps. So does annealing options must
be

annealing = single single single
annealing_npoints = 5 5 5
annealing_time = 0 25 50 75 100 0 25 50 75 100 0 25 50 75 100

annealing_temp = 300 310 320 330 340 350 300 310 320 330 340 350 300 310
320 330 340 350
# this means that for each group temperature increase on 10K on each step
and there are 5 steps for each grou ( equal to npoints)

Does this ecxample correct or there are some connection between that values
for diffent groups ?

2) How I can couple this annealing options with the *gen_temp* values wich
as I understood must also differs on the each step ? OR should I use some
averaged gen_temp?

James


4 апреля 2012 г. 16:05 пользователь Justin A. Lemkul написал:

>
>
> It can be done in one .mdp file with the simulated annealing feature.
>
>
>  Finally what exactly is tau_t time constant?
>>
>>
> See manual section 3.4.8.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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Re: [gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

Justin,


1) I've defined 5 steps for specified definition of the time of each step
as well as for more flexibile controle of the such annealing: e.g I want
that equilibration step corresponded to the temperature between 320 and
330K will be longer than between first step corresponded to 300-310K etc


2) About velosities. As I understood for annealing equilibration gen_temp
must be equal to the starting temperature of such equilibration ( gen_temp=
300 in the above example). But in what exactly circumstances the changing
in gen_temp could be usefull? As I've told after such annealing
equilibration I want to simulate my system on the high temperature
condition for efficient conformation sampling. Might it be that initial
high velocities could be usefull for such sampling efficacy?

James


4 апреля 2012 г. 17:25 пользователь Justin A. Lemkul написал:

>
>
> James Starlight wrote:
>
>> Justin,thanks!
>>
>>
>> 1) For example for the situation presented in manual for 2 groups with 3
>> and 4 points the time enty should be
>>
>> annealing_time = 0 3 6 0 2 4 6
>>
>> from this I've understood that 0 value is the start of timer for each
>> group and subsequent values are the actual time in the ps, havennt it ?
>>
>>
> Yes.
>
>
>  For example I'd like to perform nvt simulation ( with overal time 100ps)
>> for three different groups in 5 equal steps. So does annealing options must
>> be
>> annealing = single single single
>> annealing_npoints = 5 5 5
>> annealing_time = 0 25 50 75 100 0 25 50 75 100 0 25 50 75 100
>>
>> annealing_temp = 300 310 320 330 340 350 300 310 320 330 340 350 300 310
>> 320 330 340 350
>> # this means that for each group temperature increase on 10K on each step
>> and there are 5 steps for each grou ( equal to npoints)
>>
>>
> I don't understand why 5 steps are necessary.  You're doing a linear
> increase from 300K to 350K for all groups over 100 ps.  All you need is:
>
>
> annealing = single single single
> annealing_npoints = 2 2 2
> annealing time = 300 350 300 350 300 350
>
>  Does this ecxample correct or there are some connection between that
>> values for diffent groups ?
>>
>> 2) How I can couple this annealing options with the *gen_temp* values
>> wich as I understood must also differs on the each step ? OR should I use
>> some averaged gen_temp?
>>
>>
> The value of gen_temp is only used for initial velocity generation, so in
> your case it should still be set to 300.  After that, it is irrelevant.  Do
> you mean ref_t?  In this case, the annealing temperature values override
> ref_t, so it doesn't matter.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
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[gmx-users] Monitoring of Salt bridges during simulation Run

[James Starlight]

Dear Gromacs Users!


I'd like to monitor origin and destabilisation of salt-bridges during
simulation time. In particular I want to define some charged residues
within selection groups to monitor both of intra-protein as well as
protein-protein interactions. In past I've used only
g_hbondutillity to
monitor Hbonds within selection. Is there any specified program
for such task but with salt-bridges only ?


Thanks for help,

James
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Re: [gmx-users] Monitoring of Salt bridges during simulation Run

[James Starlight]

Bharat, Peter thanks for advises

I've checked g_saltbr but not found possible definition of the specified
regions ( this utility lacks -n index.ndx option). How I could ignore
contacts between solvent and protein ?

Also what is the real *-t value should I provide ? As I understood this is
only Rmin but could I define Rmax cutoff as well?

James
*
5 апреля 2012 г. 12:36 пользователь Peter C. Lai  написал:

> g_saltbr?
>
> If you have salt bridges you already know about and want to look at, you
> can always go with g_dist per pair manually.
>
> On 2012-04-05 12:23:02PM +0400, James Starlight wrote:
> > Dear Gromacs Users!
> >
> >
> > I'd like to monitor origin and destabilisation of salt-bridges during
> > simulation time. In particular I want to define some charged residues
> > within selection groups to monitor both of intra-protein as well as
> > protein-protein interactions. In past I've used only
> > g_hbond<http://manual.gromacs.org/online/g_hbond.html>utillity to
> > monitor Hbonds within selection. Is there any specified program
> > for such task but with salt-bridges only ?
> >
> >
> > Thanks for help,
> >
> > James
>
> > --
> > gmx-users mailing listgmx-users@gromacs.org
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>
>
> --
> ==
> Peter C. Lai| University of Alabama-Birmingham
> Programmer/Analyst  | KAUL 752A
> Genetics, Div. of Research  | 705 South 20th Street
> p...@uab.edu | Birmingham AL 35294-4461
> (205) 690-0808  |
> ==
>
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[gmx-users] MD after equilibration phase

[James Starlight]

Dear Gromacs users!


I have small question about order of the runs and input data.

Ussually I do 2 equilibration phases and subsequent productive phase in the
conditions wich are equal to the last equilibration phase ( e.g often this
is npt ).

In the second equil.mdp and md.mdp there is option

continuation = yes

which means that there have been previous phases of the simulation from
wich  coordinates and velocities should be taken.

As I understood the coordinates is taken from .gro file but from what file
the velocities must be providen ? Does it .cpt checkpoint file from
previous run? In some cases I've forgotten to define -t npt.cpt for my MD
run providing only coordinates in GRO file, topology and md.mdp but I have
not seen any errors in such simulation due to absence of that .cpt and
GROMPP never remind me of the absense of this file. What exactly is in that
.cpt file and from wich source the velocities from equilibration phase are
taken ?

James
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Re: [gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

By the way I've completed equilibration phase of my system ( receptor in
Ccl4-water membrane mimicking layer) in the hight temperature conditions. :)

During 3ns I gradually increased temperature from 300 to 700k with posres
applied on the Ccl4 C atoms and all atoms of protein. After this I've
changed posres applied on the protein to the backbone atoms only and
started gradually decrease fc falue ( from 1000 to 250 ). The overal system
was stabile and I've noticed linnear increase of the total energy
accompanied by such increase of temperature.

Than  When I've removed posres from side-chains I've noticed bigger RMSD in
potential energy of my system.

The only artifact that I've noticed is that some water was moved into the
Ccl4 layer during this equilibration. How I could prevent such layer mixing
without applying posres on water? I need free-water in my system because I
want to see how some water move into the receptor that have a chanell wich
some internal- water cavities having functional meaning.
Does some operation with the COM option could prevent mixing of some
differen solvent layers ?
At the curent moment I've difined COM as

Protein_CCl4 SOL_NA_CL_XW

where XW is the water observed in the X-ray structure of that protein (
I've defined that mollecules in separate layer)

Thanks for help

James


4 апреля 2012 г. 18:14 пользователь Justin A. Lemkul написал:

>
>
> James Starlight wrote:
>
>> Justin,
>>
>>
>> 1) I've defined 5 steps for specified definition of the time of each step
>> as well as for more flexibile controle of the such annealing: e.g I want
>> that equilibration step corresponded to the temperature between 320 and
>> 330K will be longer than between first step corresponded to 300-310K etc
>>
>>
> OK, that makes sense.  What you showed before does not do that, hence my
> confusion.
>
>
>
>> 2) About velosities. As I understood for annealing equilibration gen_temp
>> must be equal to the starting temperature of such equilibration ( gen_temp=
>> 300 in the above example). But in what exactly circumstances the changing
>> in gen_temp could be usefull? As I've told after such annealing
>> equilibration I want to simulate my system on the high temperature
>> condition for efficient conformation sampling. Might it be that initial
>> high velocities could be usefull for such sampling efficacy?
>>
>>
> I'm not clear on what you're asking.  If you are generating velocities
> (which you wouldn't after you reach your target via SA or equilibration),
> then you don't need gen_temp or gen_vel.  If you're starting a new run,
> then gen_temp should be equal to the ref_t value you wish to use for the
> simulation.  If your gen_temp and ref_t values are not the same, then it is
> quite possible that the simulation will crash or give very unexpected
> results due to potential instabilities in the thermostat algorithm.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
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Re: [gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

Mark,



> If you make your layer boundaries perpendicular to some axis then you can
> use position restraints on water oxygens that have non-zero force constants
> only with respect to that axis. Then relax the water position restraints
> before any others.
>
>
Yes, I've thought about this to apply posres onto selected coordinates to
allow waters move only laterally relavitely protein-membrane-like system.
But this prevent to move water into the receptor interious as well so it's
not very good aproach.

Also I've thought about vary of the ref_t oprions wich I've defined
separatelly for protein_membrane layer and for water_ions. As I've told I
want to increase confoprmation sampling of my protein by means of gradually
temperature increasing. Could I rise only ref_t for the protein_ccl4 layer
with the apllied posres on the protetn (backbone atoms) and ccl4 ( C atoms)
during nvt equilibration while not changing ref_t for water and ions ? Will
my system be some unphysicall in that case ?  Or as the alternative way
could I decrease ref_t for the water_ions layer in the end of nvt
equilibration to allow water to move out from the Ccl4 layer?



James
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Re: [gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

Mark,





> Assuming you're raising your temperature during equilibration and then
> running at high temperature, then you don't want water moving into the
> receptor interior during equilibration for the same reason you didn't want
> water moving into the CCl4. And you're going to run further equilibration
> after taking off all the restraints anyway, right? And if water moves into
> the receptor interior, then it probably does that under high-temperature
> equilibrium conditions...
>

It is that I want to prevent movement of water into Ccl4 layer (that is
drive by the increased temperature and have not been present in the natural
conditions) but allow it to move into the receptor interiour ( that is
normally observed experimentally). So the posres application may prevent
water to move both into the receptor and Ccl4 so this aproach could not be
useful in my case, couldn't it ?



>
> On point, the reference temperature has little to do with whether phases
> diffuse into (or out of) each other, and lots to do with what ensemble you
> might be sampling. The actual temperature controls the rate of such
> diffusion, of course, but if the non-bonded interactions allow for
> intermixing, then you'll get some degree of that regardless of any other
> setting. You'd be well advised to check that your CCl4-water boundary
> behaves acceptably before you invest in the protein simulation...
>

Specifically I've desided to rise temperature of my system to increase
conformation sampling of the protein surrounded of the interiour. For this
I've devided my system on several parts to couple to separate thermostates.
One part is the protein and CCl4 layer wich mimick the membrane and another
part is the sorrounded water ( SOL), internal water ( wich may present in
the protein interiour transitory but never in the Ccl4 layer) and IONS (
wich are always in the SOL layer). In order that increase the rate of
conformation sampling I've gradually increased ref_t of each t_group. In
part this result in evaporation of water and some of that water has moved
in Ccl4 layer. So its intresting for me might  I set ref_t for water_ions
group as the specified value ( ref_t= 310 k) and gradually increase only
ref_t for the protein_ccl4 group in the annealing manner. As the
consequence I want to prevent evaporation of the water but maintain of the
overal temperature high of my system tp increase sampling of the protein
conformation ?

I inderstand that such aproach is very unphysical but aplication of the
posres and other tricks are from this theme but works good in some cases :)


James


> Mark
>
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Re: [gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

Justin,

Could you tell me for what purposes the definition of the several ref_t
values could be usefull? Does this just for measurements of the temperature
during simulation for each group separately or is there something else?


By the way as I've found in literature another important question about
such simulation in high temperature conditions is the selection of the
integrator algorithm wich also could enhanse sampling under this
conditions.  E.g I've found that the BD integrator could be more usefull
than leap-frog MD. What timestep and other importnat options defined in mdp
should be tken into account within simulation with BD ? I've never perform
simulations with this integrator and could not realise how it could enhanse
simulation rate in comparison to the MD and what artifacts should expect
from that :)


James

9 апреля 2012 г. 22:31 пользователь Justin A. Lemkul написал:

>
>
> James Starlight wrote:
>
>> Mark,
>>
>>
>>
>>
>>
>>Assuming you're raising your temperature during equilibration and
>>then running at high temperature, then you don't want water moving
>>into the receptor interior during equilibration for the same reason
>>you didn't want water moving into the CCl4. And you're going to run
>>further equilibration after taking off all the restraints anyway,
>>right? And if water moves into the receptor interior, then it
>>probably does that under high-temperature equilibrium conditions...
>>
>>
>> It is that I want to prevent movement of water into Ccl4 layer (that is
>> drive by the increased temperature and have not been present in the natural
>> conditions) but allow it to move into the receptor interiour ( that is
>> normally observed experimentally). So the posres application may prevent
>> water to move both into the receptor and Ccl4 so this aproach could not be
>> useful in my case, couldn't it ?
>>
>>
>>
>
> No, it wouldn't.  I don't understand why you believe some water absolutely
> can't leak into the CCl4 layer, at least transiently.  If you're getting
> massive mixing, then that's a problem for which I don't know a clear
> solution in this case.  Occasional leakage is not unexpected, as it even
> occurs in lipid bilayers.  True, water and CCl4 are not particularly
> miscible, but to say that they should remain 100% isolated in reality is
> not correct.
>
>
>
>>
>>On point, the reference temperature has little to do with whether
>>phases diffuse into (or out of) each other, and lots to do with what
>>ensemble you might be sampling. The actual temperature controls the
>>rate of such diffusion, of course, but if the non-bonded
>>interactions allow for intermixing, then you'll get some degree of
>>that regardless of any other setting. You'd be well advised to check
>>that your CCl4-water boundary behaves acceptably before you invest
>>in the protein simulation...
>>
>>
>> Specifically I've desided to rise temperature of my system to increase
>> conformation sampling of the protein surrounded of the interiour. For this
>> I've devided my system on several parts to couple to separate thermostates.
>> One part is the protein and CCl4 layer wich mimick the membrane and another
>> part is the sorrounded water ( SOL), internal water ( wich may present in
>> the protein interiour transitory but never in the Ccl4 layer) and IONS (
>> wich are always in the SOL layer). In order that increase the rate of
>> conformation sampling I've gradually increased ref_t of each t_group. In
>> part this result in evaporation of water and some of that water has moved
>> in Ccl4 layer. So its intresting for me might  I set ref_t for water_ions
>> group as the specified value ( ref_t= 310 k) and gradually increase only
>> ref_t for the protein_ccl4 group in the annealing manner. As the
>> consequence I want to prevent evaporation of the water but maintain of the
>> overal temperature high of my system tp increase sampling of the protein
>> conformation ?
>>
>> I inderstand that such aproach is very unphysical but aplication of the
>> posres and other tricks are from this theme but works good in some cases :)
>>
>>
>>
> This sounds really fishy to me.  Coupling different parts of a system to
> thermostats at different temperatures just begs for artifacts.  The use of
> thermostats for separate parts of the system, even at the same temperature,
> is questionable since you violate energy conservation.  Of course, for many
> cases, they're a necessity and

Re: [gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

Justin,


10 апреля 2012 г. 16:21 пользователь Justin A. Lemkul написал:

>
> I have never used the bd integrator so I cannot offer any help here.  I
> don't see any magical reason why you should expect it to enhance sampling
> though.


 I've found in the literature that this integrator could rise the
integration-time-step from common 1-2fs used with the MD-integrator.



By the way I've tried to test my system equilibrated in the hight
temperature in different conditions. As the consequence when I've removed
all posres ( on the last stage of equilibration it's value was 200 for
backbone atoms only) from my protein the alpha helixes have been
destabilised already after 3ns of such unconstrained simulation ( ref_t=
700k).

So I suppose that the presence of the some constrained factor is needed to
prevent destabilisation but allow conformation sampling.  I see three
alternative ways of my production MD run with enhanced sampling.

1- First of all as the most trivial way I'm thinking of using soft posres
applied on backbone atoms only with the constained value ( 50-100 kj*nm2)
corresponded to the energy of the thermal motion.

2- Also I've thought about application of the harmonic distance_restraince
(instead of posres) on the all backbone atoms exept of flexible loops where
this disres must be in the longer range ( e.g up to 15-20A) but I could not
realise about usefullness of such aproach because I cant define value for
such disres for the atoms in helixes. It's known that conformation
transitions wich I want to ssample accompanied by the large scale motions
in the helical segments ( up to 10-15 A). At the same time such big
fluctuations on the other atoms may destabiise regions wich are more rigid.
Should I define several sets of restrains for my protein to allow one
regions move with bigger amplitudes in comparison with rigid fragments ?

3- Finally alternative aproach is the ussage of common temperature (
ref_t=310k) in the production run but using starting velocities obtained
from the nvt equilibrration obtained with the hight ( 700k) temperature.
Can I enhance sampling using that starting conditions ?


What from this three strategies is the most suitable? IS there any
alternative ways for such high-temperature simulation ?


Thanks for help again,


James
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Re: [gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

Justin,


I have not quite sure about methodology of aplication of such harmonic
distance restrains yet.

E.g I want to constraint distancec of the backbone atoms of my protein
within 7 A ( to allow deviation of all backnones up to 7 A)

I've tried

genrestr -f start.gro -n index.ndx -disre -disre_dist 0.7 -disre_frac 0.7
-disre_up2 1.0

>From this I've obtained for first 5 backbone atoms below disres

1 5 1 0  1  0.0441928   0.2504261.25043  1
110 1 1  1  0.0697795   0.3954171.39542  1
112 1 2  1   0.101657   0.5760591.57606  1
114 1 3  1   0.138237   0.7833411.78334  1
115 1 4  1   0.160509   0.9095541.90955  1

so the atoms 1 and 5 would be unconstrained if the distance between them
would be 0.004-0.25, atoms 1 and 10 would be constrained within distance
0.069-0.395 etc.

I'm not quite understood from manual if  the disre_dist exactly that range
value ralative atom coordinate in the start.gro ? What is the -desre_frac
and in what cases in could be usefull ?


James

10 апреля 2012 г. 18:25 пользователь Justin A. Lemkul написал:

>
>
>  So I suppose that the presence of the some constrained factor is needed
>> to prevent destabilisation but allow conformation sampling.  I see three
>> alternative ways of my production MD run with enhanced sampling.
>>
>> 1- First of all as the most trivial way I'm thinking of using soft posres
>> applied on backbone atoms only with the constained value ( 50-100 kj*nm2)
>> corresponded to the energy of the thermal motion.
>>
>> 2- Also I've thought about application of the harmonic
>> distance_restraince (instead of posres) on the all backbone atoms exept of
>> flexible loops where this disres must be in the longer range ( e.g up to
>> 15-20A) but I could not realise about usefullness of such aproach because I
>> cant define value for such disres for the atoms in helixes.
>>
>
> Sure you can.  Use genrestr with a suitable index group.  The use of lots
> of distance restraints precludes the use of DD, so you're limited to using
> mdrun -pd, which is a lot slower and may counteract any perceived benefit
> in terms of simulation time.
>
>
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Re: [gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

Tsjerk,

Thank you for suggestions!


Indeed the hight temperature ( I'm using 700K) which I use for enhansing
sampling rate  resulted in destabilisation of the secondary structure.

To prevent this I've used two slightly different aproaches based on the
restraint. But in both cases I've used slightly soft restrains with
fs=10-200.

The first aproach is the ussage of the posres applied on each backbone atom
with fc=10-50. I've tested case with fc=50 and found that such restrains
were very hight. I've not noticed any conformation sampling of my protein (
rmsd of backbone < 0.3 nm) during 10ns of such simulation. So I've decided
to test a case with fc=10 ( under calculation)

The second approach is the application of the harmonic distance restrainse
wich I've applied on each backbone atom pair in the CUTOFF radius of 1.0
nm. The Rc value was chosen because of my protein is the 7 buddle of alpha
helices so this aproach could be usefull but exactly value for R have been
chosen empirically. I've selected deviation value wich are equal to 1\2 of
cutoff radius = 1.5 nm. I have not realise whaat I could obtain yet from
this because I'm not quite sure about coccect values of such disres.


James

11 апреля 2012 г. 13:35 пользователь Tsjerk Wassenaar
написал:

> Hey :)
>
> I'd say a protein should be loosing structure at 700K. Can't even say
> the force field is wrong there, even though it hasn't been
> parameterized for such temperatures for certain. You'd have to check
> with experiments.
> Trying to do high-temperature simulations is fine. But trying to do
> high temperature simulations to get results that match a room/body
> temperature ensemble is completely bogus. If you aim to use this
> approach for enhanced sampling, you're in for some serious
> reparameterization. Part of the deal may indeed be adding
> long(er)-range distance restraints. However, the force constants to
> use will increase with temperature, and with very high temperatures
> the force constants may end up so high that they give rise to fast
> oscillations, which will require using a smaller time step.
>
> Just my 2 cents...
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

Tsjerk,


As Justin already has noticed there were lot of examples of implementation
of the high temperature aproach to increase conformation sampling. This
could be usefull because of short time-scale of typical MD trajectory and
hight energy barriers of the adjacent energy-minimums wich could correspond
to the functional-relevant conformations.  So the main reason of such
stimulations in to dicrease such barriers to promote transitions to the
functional-relevant states conformations Finally I can sample the output of
such simulation and compare this resulted conformations with the
experimental data. If I obtain good similarity this may indicate about
efficiency of such aproach

On other hand such simulation could result in some non-native conformations
due to the non-native condtions. So the artificial restrains like as the
distance restrains within native conformation ( obttained by NMR for
instance) could be usefull-aproach to keep the system in the native-like
conformations while enhansing sampling of the native-like structures via
rising of temperatures. So combinations of  such tricks could give
physical-relevant results partly couldn't it ? However I suppose that the
main disadvantage of such aproach is the non-physical intermediate states
produced by non-native transitions pathways wich could arrise from such
simulation.



James

11 апреля 2012 г. 18:09 пользователь Tsjerk Wassenaar
написал:

> Hey James,
>
> Have you thought about the physical relevance of your results?
>
> Cheers,
>
> Tsjerk
>
> On Wed, Apr 11, 2012 at 12:01 PM, James Starlight
>  wrote:
> > Tsjerk,
> >
> > Thank you for suggestions!
> >
> >
> > Indeed the hight temperature ( I'm using 700K) which I use for enhansing
> > sampling rate  resulted in destabilisation of the secondary structure.
> >
> > To prevent this I've used two slightly different aproaches based on the
> > restraint. But in both cases I've used slightly soft restrains with
> > fs=10-200.
> >
> > The first aproach is the ussage of the posres applied on each backbone
> atom
> > with fc=10-50. I've tested case with fc=50 and found that such restrains
> > were very hight. I've not noticed any conformation sampling of my
> protein (
> > rmsd of backbone < 0.3 nm) during 10ns of such simulation. So I've
> decided
> > to test a case with fc=10 ( under calculation)
> >
> > The second approach is the application of the harmonic distance
> restrainse
> > wich I've applied on each backbone atom pair in the CUTOFF radius of 1.0
> nm.
> > The Rc value was chosen because of my protein is the 7 buddle of alpha
> > helices so this aproach could be usefull but exactly value for R have
> been
> > chosen empirically. I've selected deviation value wich are equal to 1\2
> of
> > cutoff radius = 1.5 nm. I have not realise whaat I could obtain yet from
> > this because I'm not quite sure about coccect values of such disres.
> >
> >
> > James
> >
> > 11 апреля 2012 г. 13:35 пользователь Tsjerk Wassenaar  >
> > написал:
> >>
> >> Hey :)
> >>
> >> I'd say a protein should be loosing structure at 700K. Can't even say
> >> the force field is wrong there, even though it hasn't been
> >> parameterized for such temperatures for certain. You'd have to check
> >> with experiments.
> >> Trying to do high-temperature simulations is fine. But trying to do
> >> high temperature simulations to get results that match a room/body
> >> temperature ensemble is completely bogus. If you aim to use this
> >> approach for enhanced sampling, you're in for some serious
> >> reparameterization. Part of the deal may indeed be adding
> >> long(er)-range distance restraints. However, the force constants to
> >> use will increase with temperature, and with very high temperatures
> >> the force constants may end up so high that they give rise to fast
> >> oscillations, which will require using a smaller time step.
> >>
> >> Just my 2 cents...
> >>
> >> Tsjerk
> >>
> >> --
> >> Tsjerk A. Wassenaar, Ph.D.
> >>
> >> post-doctoral researcher
> >> Molecular Dynamics Group
> >> * Groningen Institute for Biomolecular Research and Biotechnology
> >> * Zernike Institute for Advanced Materials
> >> University of Groningen
> >> The Netherlands
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> >> htt

Re: [gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

At the current stage I want to understand how to apply such disres in
relation to the current starting structure without external experimental
data.

E.g. I have some initial structure for wich I'd like to generate disres
applied on each backbone atom within some cutoff radius. As the consequence
I want that this set of disres were generated automatically assuming
deviation from this initial structure on the desired value ( as I
understood this is -disre_dist ). Does my understanding correct in general
? What is -dis_frac wich result in some shift on the defired value both of
up0 and up1 distances in the output file ?

I have complete some test run when I've applied disres in such manner with
-disre_dist 1 nm in the Rc=1nm to allow deviation of the backbone within
the same radius. As the consequence I've obtained deformed structure of my
protein. I've checked RMSD and found that deformation have occured very
rapidly but new non-native conformation was stabilised very quickly ( new
plato on rmsd diagram) and was relatively stabile during 15ns. Does the
disres were applied incorrectly or shoud I increase forses ? ( I've used
fc=100 )

James


James

11 апреля 2012 г. 23:31 пользователь Tsjerk Wassenaar
написал:

> Hey James,
>
> It's reassuring to find you did think of it. The approach may have
> merits, or may be a waste of CPU. But the proof of the pudding is in
> the eating of it. The connection with NMR data makes sense. The
> restraints may be time-averaged, involving different conformational
> states, hampering the usual annealing-based structure determination.
> But room-temperature simulations may not allow the transitions
> required. Hence, applying the same restraints at an elevated
> temperature, probably using a higher force constant, could yield the
> desired ensemble. To get a room-temperature ensemble by using some
> restraints will probably not work, but it's an interesting list of
> things that shouldn't have worked according to some, yet worked out
> for those who tried :p Nonetheless, applying local restraints to
> maintain integrity and use an elevated temperature to enhance
> conformational sampling, might actually also be a valuable approach.
> Good luck :)
>
> Tsjerk
>
> On Wed, Apr 11, 2012 at 8:27 PM, James Starlight 
> wrote:
> > Tsjerk,
> >
> >
> > As Justin already has noticed there were lot of examples of
> implementation
> > of the high temperature aproach to increase conformation sampling. This
> > could be usefull because of short time-scale of typical MD trajectory and
> > hight energy barriers of the adjacent energy-minimums wich could
> correspond
> > to the functional-relevant conformations.  So the main reason of such
> > stimulations in to dicrease such barriers to promote transitions to the
> > functional-relevant states conformations Finally I can sample the output
> of
> > such simulation and compare this resulted conformations with the
> > experimental data. If I obtain good similarity this may indicate about
> > efficiency of such aproach
> >
> > On other hand such simulation could result in some non-native
> conformations
> > due to the non-native condtions. So the artificial restrains like as the
> > distance restrains within native conformation ( obttained by NMR for
> > instance) could be usefull-aproach to keep the system in the native-like
> > conformations while enhansing sampling of the native-like structures via
> > rising of temperatures. So combinations of  such tricks could give
> > physical-relevant results partly couldn't it ? However I suppose that the
> > main disadvantage of such aproach is the non-physical intermediate states
> > produced by non-native transitions pathways wich could arrise from such
> > simulation.
> >
> >
> >
> > James
> >
> > 11 апреля 2012 г. 18:09 пользователь Tsjerk Wassenaar  >
> > написал:
> >
> >> Hey James,
> >>
> >> Have you thought about the physical relevance of your results?
> >>
> >> Cheers,
> >>
> >> Tsjerk
> >>
> >> On Wed, Apr 11, 2012 at 12:01 PM, James Starlight
> >>  wrote:
> >> > Tsjerk,
> >> >
> >> > Thank you for suggestions!
> >> >
> >> >
> >> > Indeed the hight temperature ( I'm using 700K) which I use for
> enhansing
> >> > sampling rate  resulted in destabilisation of the secondary structure.
> >> >
> >> > To prevent this I've used two slightly different aproaches based on
> the
> >> > restraint. But in both cases I've used slightly soft restrains with
> >

[gmx-users] Simulation of the pure lipid bilayer

[James Starlight]

Dear Gromacs Users!


I want to perform simulation of the pure bilayer surrounded by water. I'm
using already pre-equilibrated bilayers as the initial structure. During
conversion pdb-> gro -> pdb the velocities from initial equilibration runs
of the structure were lost. Should I start generating this velocities in my
production run ( gen_Vel= yes) or i must do equilibration instead first to
generate velocities? Finally what length should this equilibration be to
provide reasonable velocities for futrher MD run if I would avoild long
equilibration period because of suitability of my initial model?


Thanks for help,


James
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Re: [gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

Dear Gromacs Users!

By that moments I've completed 2 sets of simulation in high temperature

1- With applied posres on the backbone atoms ( fc= 200 ).

The result was- that the posres prevented motion of the helixes as the
rigid bodies so I've not noticed any conformation sampling.

Question : Could I observe some conformation sampling on that trajectory by
means of some external tricks ? E.g extracting of the eigenvectors via PCA?

2 With applied network of disres applied on backbone atoms of the helix
elements of my protein within Rc=1nm.

As the result of that simulation I've observed distortion of my protein
wich resulted in some kind of shrinking of the helix elements.

Question :  How I could specify that disres more correctly ? If I've
observed some kind of shrinking of my protein does it means that Rc was
chosen incorectly or should I define disres in anothe manner ? ( I'have not
quite understand what exatly is the R_fract and in what situation it could
be useful ).

James
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Re: [gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

Justin,


I've applied disres on each backbone atom of my potein within cutoff
distance of 1nm ( Rc=1.0 nm). I've selected this value for cutoff to
decrease overall ammount of the restains in my itp file. Also such value (
1nm) was selected because of the relatively tight packing of the alpha
helices in the TM buddle of membrane protein.

The selected values for disre_dist, disre_up2 and disre_frac were 1, 1.2
and 0.5 nm respectually . Also I've made disres with 1 and 0 nm values but
I have not noticed any difference in the resulted behaviour of the
constrained system. As the consequence I have not clearly realise what
exactly is the disre_frac and in what exactly cases this option could be
helpfull.


This is an example of my output itp file

[ distance_restraints ]
;   i j ? label  funct loup1up2 weight
1 5 1 0  1  01.647312.64731  1
110 1 1  1  0 1.7326 2.7326  1
112 1 2  1  01.838862.83886  1
114 1 3  1  01.960792.96079  1
115 1 4  1  02.035033.03503  1
117 1 5  1  01.990072.99007  1
119 1 6  1  02.088793.08879  1
127 1 7  1  02.139163.13916  1
129 1 8  1  02.271473.27147  1
130 1 9  1  02.357933.35793  1


I've made 10 ns simulation of such system and observe rapid shrinking of my
protein starting with first 100ps like the distances that I chose were too
small and forces shrink my protein. But when I've tried larger distance
value for disre_dist my protein denatured rapidly as no disres were
presented.

So the main question is How I could specify this disre values if I want to
restrain the motion of the helixes of my protein within disre value ( e.g
10 A) relatively current confrmation ?


James

16 апреля 2012 г. 15:05 пользователь Justin A. Lemkul написал:

>
>
> James Starlight wrote:
>
>> Dear Gromacs Users!
>>
>> By that moments I've completed 2 sets of simulation in high temperature
>>
>> 1- With applied posres on the backbone atoms ( fc= 200 ).
>>
>> The result was- that the posres prevented motion of the helixes as the
>> rigid bodies so I've not noticed any conformation sampling.
>>
>> Question : Could I observe some conformation sampling on that trajectory
>> by means of some external tricks ? E.g extracting of the eigenvectors via
>> PCA?
>>
>>
> If you've restrained the position of the atoms, there's no trick that can
> magically give you a more desirable result.  You've limited the ability of
> atoms to move, plain and simple.
>
>
>  2 With applied network of disres applied on backbone atoms of the helix
>> elements of my protein within Rc=1nm.
>>
>>
> What does Rc mean here?
>
>
>  As the result of that simulation I've observed distortion of my protein
>> wich resulted in some kind of shrinking of the helix elements.
>>
>> Question :  How I could specify that disres more correctly ? If I've
>> observed some kind of shrinking of my protein does it means that Rc was
>> chosen incorectly or should I define disres in anothe manner ? ( I'have not
>> quite understand what exatly is the R_fract and in what situation it could
>> be useful ).
>>
>>
> Without seeing your [distance_restraints] directive, it's impossible to
> comment aside from saying that if your structure distorted severely, then
> yes, you did something wrong.  I also don't know what R_fract is.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
> --
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> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
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>  posting!
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> Can't post? Read 
> http://w

Re: [gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

Justin,


Thank you for explanation. Tomorrow I'll try to check results of simulation
with the disres applied with its default values as well as with narrower
-disre_dist values ( ignorring -disre_frac option at all )  and post here
results of such simulations.


1) The cut-off distance wich I've specified was defined with the genrest
comand with the -cutoff 1.0 flag. Finally all restrains were apllied on the
backbone atoms of alpha helices of the Transmembrane domain of my protein
wich I've defined in the index.ndx file. So all loops of my protein were
not-restrained at all.

Also I have some small  question about size of output edr file. I've
noticed that size of this files of such simulations  (with the disres
applied as well as with the -pd flag ) is a very big ( 10-15 gb) Why this
occurs and how I could fix it?



thanks again for help,


James

16 апреля 2012 г. 17:36 пользователь Justin A. Lemkul написал:

>
>
> James Starlight wrote:
>
>> Justin,
>>
>>
>> I've applied disres on each backbone atom of my potein within cutoff
>> distance of 1nm ( Rc=1.0 nm). I've selected this value for cutoff to
>> decrease overall ammount of the restains in my itp file. Also such value (
>> 1nm) was selected because of the relatively tight packing of the alpha
>> helices in the TM buddle of membrane protein.
>>
>>
> I still don't see how you're defining this cutoff anywhere in genrestr or
> any other step.  Do you have some special index group that you're using in
> your genrestr command?  It may not be relevant, I'm just very confused.
>
>
>  The selected values for disre_dist, disre_up2 and disre_frac were 1, 1.2
>> and 0.5 nm respectually . Also I've made disres with 1 and 0 nm values but
>> I have not noticed any difference in the resulted behaviour of the
>> constrained system. As the consequence I have not clearly realise what
>> exactly is the disre_frac and in what exactly cases this option could be
>> helpfull.
>>
>>
> The -disre_dist option sets the tolerance for defining the 'lo' value.  By
> default, it is a fixed distance below the actual distance contained in the
> coordinate file.  The default value is 0.1, so if your distance is 0.5, the
> 'lo' value is set to 0.4 (i.e. 0.5 - 0.1).  When using the -disre_frac
> value, the value specified in -disre_dist is ignored, so be aware that when
> you combine the two, you override -disre_dist (as stated in genrestr -h).
>  So if you're using -disre_frac of 0.5, your 'lo' value for a 0.5-nm
> distance is 0.25.
>
>
>
>> This is an example of my output itp file
>>
>> [ distance_restraints ]
>> ;   i j ? label  funct loup1up2 weight
>>1 5 1 0  1  01.647312.64731  1
>>110 1 1  1  0 1.7326 2.7326  1
>>112 1 2  1  01.838862.83886  1
>>114 1 3  1  01.960792.96079  1
>>115 1 4  1  02.035033.03503  1
>>117 1 5  1  01.990072.99007  1
>>119 1 6  1  02.088793.08879  1
>>127 1 7  1  02.139163.13916  1
>>129 1 8  1  02.271473.27147  1
>>130 1 9  1  02.357933.35793  1
>>
>>
>> I've made 10 ns simulation of such system and observe rapid shrinking of
>> my protein starting with first 100ps like the distances that I chose were
>> too small and forces shrink my protein. But when I've tried larger distance
>> value for disre_dist my protein denatured rapidly as no disres were
>> presented.
>>
>>
> The problem here is that you're allowing all distances between 0 and 'up1'
> to experience zero restraining force.  That gives the system incredibly
> wide latitude and basically makes the restraints useless.  What you're
> calling either shrinking or denaturing are likely just two possible
> outcomes from the structure being destabilized in some way.  Try running
> genrestr with default options to see if you get a better result.
>
>
>  So the main question is How I could specify this disre values if I want
>> to restrain the motion of the helixes of my protein within disre value (
>> e.g 10 A) relatively current confrmation ?
>>
>>
> Are you wanting the restraints to be maintained within a 1-nm distance of
> their current value? 

Re: [gmx-users] Re: Simulation in the high temperature conditions

[James Starlight]

Justin,


I've tested default disres applied to my protein under high temperature
condiitions.

I've observed that default disre_dist as well as its values up to 0.3 nm in
general prevent destabilisation of my protein under non-native conditions
allowing some dynamics of the restrained regions ( I've not used disre_frac
in all this experiments). But starting from the values of 0.5 nm my protein
was perturbed again.

So the remained questions are

1) Firstly  I'd like to test different cutoff radii for the
increasing\decreasing number of disres but I didnt know how exactly define
this value more accuracy ( previously I've used such cutoff radius for
normal mode analysis of such protein ( in thact case Rc define contacts
between C-alpha atoms ) where the value of 0.8-1 nm gave me good results).

2) My protein consist of some internal water mollecules wich I've defined
explicitly as the separate group (I've coppied coordinates of such waters
from the X-ray structure ).  During dynamics RUN I've noticed that some of
this waters were moved out from receptor to the SOL layer and only several
waters remined in the bounded state with the interoiour of my protein. How
I could specify T_couple and COM groups for such internal waters most
accyracy? I've tried to define it as the part of SOL_Ions layer as well as
in the common group with the protein for both the T_coupling and COM but I
have not noticed any difference between that simulations.


Thanks for help again,


James

16 апреля 2012 г. 18:09 пользователь Justin A. Lemkul написал:

>
>
> James Starlight wrote:
>
>> Justin,
>>
>>
>> Thank you for explanation. Tomorrow I'll try to check results of
>> simulation with the disres applied with its default values as well as with
>> narrower -disre_dist values ( ignorring -disre_frac option at all )  and
>> post here results of such simulations.
>>
>>
>> 1) The cut-off distance wich I've specified was defined with the genrest
>> comand with the -cutoff 1.0 flag. Finally all restrains were apllied on the
>> backbone atoms of alpha helices of the Transmembrane domain of my protein
>> wich I've defined in the index.ndx file. So all loops of my protein were
>> not-restrained at all.
>>
>>
> Ah, I see now.
>
>
>  Also I have some small  question about size of output edr file. I've
>> noticed that size of this files of such simulations  (with the disres
>> applied as well as with the -pd flag ) is a very big ( 10-15 gb) Why this
>> occurs and how I could fix it?
>>
>>
>>
> There are energy terms associated with distance restraints.  They cause
> the .edr file to get large very fast if you have a lot of them.  You'll
> have to decrease nstenergy to make the files smaller, or not use the
> restraints.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
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[gmx-users] Making Disulfide Bonds

[James Starlight]

Dear Gromacs Users!

I have a model of my protein wich has 4 S-S bounds in the loop regions. So
I want to define in topology all those four S-S linkage.

Unfortunatelly one of that S-S have not been recognised by Gromacs ( Also
I've tried to check this bond in pymol and found that distance between that
two Cys Cys are larger for S-S occurence) due to some inaccyracy of model.

Is there any way to define such missing S-S manually? On the gromacs site
I've found possible sollution by means of spechbond.dat editing. I've tried
to increase distance between S-S atoms but this have not had desirebly
affect.

In the topology.top file I've found that the S-S bonds beetween S atoms are
defined in the bond section without any type for such bond type. Also I've
found that the same enties are present in the angle and dihedralls
sections.  Could I define the same contact only in the bond section and
further minimise my system to obtain new S-S linckage or should I also
define all other enties ( like dihedralls etc) for that bond ?


Thanks for help


James
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Re: [gmx-users] Making Disulfide Bonds

[James Starlight]

Hi Francesco!

So I must define in the current topology the disres bettwen two S atoms (
in the below example 1 and 10 ) to apply hormonic restains

[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
  1 10  10 10.18 0.20 0.22 1.0

to restrain this atoms within 0.2 nm. Does it correct ? Or should I
use some other disres for such task ?

James



2012/4/28 francesco oteri 

> Hi James,
> usually people run a minimization using distance restrain on the two atoms
> in order to
> make them closer.
> Then the obtained cnfiguration is used to recalculate the topology.
>
> Francesco
>
> 2012/4/28 James Starlight 
>
>> Dear Gromacs Users!
>>
>> I have a model of my protein wich has 4 S-S bounds in the loop regions.
>> So I want to define in topology all those four S-S linkage.
>>
>> Unfortunatelly one of that S-S have not been recognised by Gromacs ( Also
>> I've tried to check this bond in pymol and found that distance between that
>> two Cys Cys are larger for S-S occurence) due to some inaccyracy of model.
>>
>> Is there any way to define such missing S-S manually? On the gromacs site
>> I've found possible sollution by means of spechbond.dat editing. I've tried
>> to increase distance between S-S atoms but this have not had desirebly
>> affect.
>>
>> In the topology.top file I've found that the S-S bonds beetween S atoms
>> are defined in the bond section without any type for such bond type. Also
>> I've found that the same enties are present in the angle and dihedralls
>> sections.  Could I define the same contact only in the bond section and
>> further minimise my system to obtain new S-S linckage or should I also
>> define all other enties ( like dihedralls etc) for that bond ?
>>
>>
>> Thanks for help
>>
>>
>> James
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
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>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
>
> --
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Re: [gmx-users] Making Disulfide Bonds

[James Starlight]

.. and the main question- what should be in mdp file of such restrained
minimisation ?

Today I've done vry properly minimisation of such system in vacuum with the
CG minimisator and applied disres ( above example ) with big force constant
( disres options have been defined in the minim.mdp file ). As the result I
have not noticed any perturbation in the distance between two S-S atoms the
distance between wich I've constrained.



2012/4/28 James Starlight 

> Hi Francesco!
>
> So I must define in the current topology the disres bettwen two S atoms (
> in the below example 1 and 10 ) to apply hormonic restains
>
> [ distance_restraints ]
> ; ai aj type index type’ low up1 up2 fac
>
>   1 10  10 10.18 0.20 0.22 1.0
>
> to restrain this atoms within 0.2 nm. Does it correct ? Or should I use some 
> other disres for such task ?
>
> James
>
>
>
> 2012/4/28 francesco oteri 
>
>> Hi James,
>> usually people run a minimization using distance restrain on the two
>> atoms in order to
>> make them closer.
>> Then the obtained cnfiguration is used to recalculate the topology.
>>
>> Francesco
>>
>> 2012/4/28 James Starlight 
>>
>>>  Dear Gromacs Users!
>>>
>>> I have a model of my protein wich has 4 S-S bounds in the loop regions.
>>> So I want to define in topology all those four S-S linkage.
>>>
>>> Unfortunatelly one of that S-S have not been recognised by Gromacs (
>>> Also I've tried to check this bond in pymol and found that distance between
>>> that two Cys Cys are larger for S-S occurence) due to some inaccyracy of
>>> model.
>>>
>>> Is there any way to define such missing S-S manually? On the gromacs
>>> site I've found possible sollution by means of spechbond.dat editing. I've
>>> tried to increase distance between S-S atoms but this have not had
>>> desirebly affect.
>>>
>>> In the topology.top file I've found that the S-S bonds beetween S atoms
>>> are defined in the bond section without any type for such bond type. Also
>>> I've found that the same enties are present in the angle and dihedralls
>>> sections.  Could I define the same contact only in the bond section and
>>> further minimise my system to obtain new S-S linckage or should I also
>>> define all other enties ( like dihedralls etc) for that bond ?
>>>
>>>
>>> Thanks for help
>>>
>>>
>>> James
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>>
>> --
>> Cordiali saluti, Dr.Oteri Francesco
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
>
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Re: [gmx-users] Making Disulfide Bonds

[James Starlight]

Francesco,

Thanks, I find your aproach very handfull :)

Justin,

in that example I've defined in minim.mdp

*disre = simple

**disre_f = 5000

in the topology.top I've included

* [ distance_restraints ]
   ; ai aj type index type’ low up1 up2 fac
  1 10  10 10.18 0.20 0.22 1.0

where 1 and 10 the numbers of the S atoms of both Cys residues. and 0.2 is
the disered distance between wich I want to obtain after such minimisation.
*


As the consequence no changes have been detected after such CG minimisation
:( What I've forgotten ?

James


*
2012/4/28 Justin A. Lemkul 

>
>
> On 4/28/12 10:08 AM, James Starlight wrote:
>
>> .. and the main question- what should be in mdp file of such restrained
>> minimisation ?
>>
>> Today I've done vry properly minimisation of such system in vacuum with
>> the CG
>> minimisator and applied disres ( above example ) with big force constant (
>> disres options have been defined in the minim.mdp file ). As the result I
>> have
>> not noticed any perturbation in the distance between two S-S atoms the
>> distance
>> between wich I've constrained.
>>
>>
> You need to add the applicable distance restraint settings for them to be
> utilized.
>
> http://manual.gromacs.org/**online/mdp_opt.html#nmr<http://manual.gromacs.org/online/mdp_opt.html#nmr>
>
> -Justin
>
>
>>
>> 2012/4/28 James Starlight > jmsstarli...@gmail.com**>>
>>
>>
>>Hi Francesco!
>>
>>So I must define in the current topology the disres bettwen two S
>> atoms ( in
>>the below example 1 and 10 ) to apply hormonic restains
>>
>>[ distance_restraints ]
>>; ai aj type index type’ low up1 up2 fac
>>
>>
>>   1 10  10 10.18 0.20 0.22 1.0
>>
>>to restrain this atoms within 0.2 nm. Does it correct ? Or should I
>> use some other disres for such task ?
>>
>>James
>>
>>
>>
>>2012/4/28 francesco oteri ><mailto:francesco.oteri@gmail.**com >>
>>
>>
>>Hi James,
>>usually people run a minimization using distance restrain on the
>> two
>>atoms in order to
>>make them closer.
>>Then the obtained cnfiguration is used to recalculate the topology.
>>
>>Francesco
>>
>>2012/4/28 James Starlight ><mailto:jmsstarli...@gmail.com**>>
>>
>>
>>Dear Gromacs Users!
>>
>>I have a model of my protein wich has 4 S-S bounds in the loop
>>regions. So I want to define in topology all those four S-S
>> linkage.
>>
>>Unfortunatelly one of that S-S have not been recognised by
>> Gromacs (
>>Also I've tried to check this bond in pymol and found that
>> distance
>>between that two Cys Cys are larger for S-S occurence) due to
>> some
>>inaccyracy of model.
>>
>>Is there any way to define such missing S-S manually? On the
>> gromacs
>>site I've found possible sollution by means of spechbond.dat
>>editing. I've tried to increase distance between S-S atoms but
>> this
>>have not had desirebly affect.
>>
>>In the topology.top file I've found that the S-S bonds
>> beetween S
>>atoms are defined in the bond section without any type for
>> such bond
>>type. Also I've found that the same enties are present in the
>> angle
>>and dihedralls sections.  Could I define the same contact only
>> in
>>the bond section and further minimise my system to obtain new
>> S-S
>>linckage or should I also define all other enties ( like
>> dihedralls
>>etc) for that bond ?
>>
>>
>>Thanks for help
>>
>>
>>James
>>
>>--
>>gmx-users mailing list gmx-users@gromacs.org
>><mailto:gmx-users@gromacs.org>
>>
>>
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>>
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>>www interface or send i

Re: [gmx-users] Coordinate file for lipid bilayer

[James Starlight]

Peter,

Thanks for advise.

I've found already pre-equilibrated POPC bilayers with 200 lipids. I've
examined that lipids and found that they are very similar to the berger's
lipids (it consists of equal nymber of atoms ) but the atom order in each
lipid is slightly different than in Tieleman's popc.itp file so during
processing of that lipids I've got error of non-matching atoms. Is there
any trivial way to make new popc.itp based on existing gro file with
correct atom order ?


James

2012/5/26 Peter C. Lai 

> Either use genbox -cs popc128b.gro or genconf -f popc128b.gro -nbox x y 0
> Tieleman's lipids require you to generate a dummy tpr for use with trjconv
> to unwrap the pbc (trjconv -s em.tpr -f popc128b.pdb -o popc128b-nopbc.gro
> -pbc mol -ur compact) first.
>
> Lots of people have their own bilayer but they may be for different FFs
> which means the atom naming would not be immediately be compatible with
> your FF; for example mine are built for charmm36 and would require atom
> renaming for another FF, even charmm27.
>
> On 2012-05-26 11:24:12AM +0400, James Starlight wrote:
> > Dear Gromacs Users!
> >
> >
> > I want to perform MD simulation of my membrane protein in POPC or POPE
> > bilayer using Tieleman's parameters for lipids by means of gromos united
> > atom force field. The main problem is that the pre-equilibrated bilayers
> > wich I found on the Dr. Tieleman's site consist of no more that 128
> lipids
> > but I want to simulate my protein with bigger number of lipids ( for
> > example starting from 200 lipids ).
> >  What should I do in that case ?  Could you provide me with  some tools
> for
> > construction of such united-atoms bilayers with desired dimensions ?
> > Finally is there any others pre-equilibrated bilayers aviable for
> > downloading besides Dr. Tieleman's site ?
> >
> >
> > thanks for your help,
> >
> > James S.
>
> > --
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> ==
> Peter C. Lai| University of Alabama-Birmingham
> Programmer/Analyst  | KAUL 752A
> Genetics, Div. of Research  | 705 South 20th Street
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[gmx-users] Measure of density in homo- and heterogeneous systems

[James Starlight]

Dear Gromacs users!


In this task I have two systems:

First system consist of single layer of Ccl4 molecules.

Second system consist of membrane-mimicking layer of Ccl4 surrounded by
water and the protein embedded in that biphastic layer.

I'd like to measure density in both of my systems to check of its packing
degree. How could I do it in the case of homo system- (where I'd like to
check density in the Ccl4 layer only) as well as in more complex hetero
system ( where I'd like to check density in each layer separately as well
as compute averaged density among all layers) ?


Thanks for advises,

James S.
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Re: [gmx-users] Measure of density in homo- and heterogeneous systems

[James Starlight]

Justin,

the main problem is the my simulation in nvt ensemble :) I understand that
density is constant in that conditions but I'd like to find way to check
this values for different components of my system.


James

2012/5/28 Justin A. Lemkul 

>
>
> On 5/28/12 3:09 PM, James Starlight wrote:
>
>> Dear Gromacs users!
>>
>>
>> In this task I have two systems:
>>
>> First system consist of single layer of Ccl4 molecules.
>>
>> Second system consist of membrane-mimicking layer of Ccl4 surrounded by
>> water
>> and the protein embedded in that biphastic layer.
>>
>> I'd like to measure density in both of my systems to check of its packing
>> degree. How could I do it in the case of homo system- (where I'd like to
>> check
>> density in the Ccl4 layer only) as well as in more complex hetero  system
>> (
>> where I'd like to check density in each layer separately as well as
>> compute
>> averaged density among all layers) ?
>>
>>
>>
> The density of the homogeneous system can easily be obtained from the .edr
> file, as long as the ensemble was NPT.  With NVT, the density term is not
> written, IIRC.
>
> In the case of the heterogeneous system, use g_density to obtain partial
> densities as a function of box dimension.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
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Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

[James Starlight]

Today I've tried to rename atoms from Swiss's params specific names to
the standard charmm names and obtain the set of the same errors
No default Improper Dih. types
No default U-B types
 No default Bond types


Its strange to me because chromophore itself consist of only one
uncommon bond  (in cyclized ring which could produce only several
additional angles and dihedrals)

By comparison in the case of Swiss atom names the total amount of the
same errors was only 9 (all erors about unknown dihedrals with
theadjacent residues. Although I've added capes in that model which
mimicks adjacent residues) it's difficult recognize suitable dihedral
types.
Do you know any others attemps to simulate GFP with chromophore in
charmm with proof parameters ?

James

2012/12/12, Justin Lemkul :
>
>
> On 12/12/12 3:11 PM, James Starlight wrote:
>> Justin,
>>
>> That errors was strange to me because I've already used Swiss's ITP
>> files for diffusional ligands including them in the topol.top of my
>> protein and there were no such errors about non-standart types in any
>> terms. It seems that some additions to the ffbonded.itp also required
>> besides the nonbonded.itp so the renaming Swiss's atoms to the CHARMM
>> would be less routinelly. I noticed some atoms types in the paper
>> which you provide me ( simulation in charmm22). Does the atom types
>> similar in both charmm fieds?
>>
>
> You probably don't get any errors because the .itp files provided to you
> from
> the server include atomtype and bonded parameter definitions that are
> internally
> self-consistent.  What you're trying to do is use the "standard" CHARMM27
> force
> field with some new molecule that has no guarantee to be fully defined under
> the
> existing force field.
>
> CHARMM22 and CHARMM27 are the same for protein parameters, with the
> exception of
> the introduction of CMAP in the latter.
>
>> Also I could not find any suitable example of CMAP for the long
>> molecule like my chromophore. I noticed that for amino acid typical
>> CMAP is the its backbone atoms as well as N and C atoms of 2 djacent
>> residues. So does the CMAP for chromophore consist of 2 strings like
>> below example or just one long strig ?
>>
>> [ cmap ]
>> -C  N  CA1  C1  N2
>> CA2 C2 N3 CA3 C
>>
>
> The proper approach would be separate strings of 5 atoms.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

[James Starlight]

Justin,

in the case of the system with the atom types assigned from that paper
the grompp produced above 118 errors of non standard bond, angle as
well as dihedral types ;o So it' seems that some 118 addition terms
must be added to the ffbonded.itp to the existing charmm parameters(
it's uncommon for me because in that case the atom names werefrom
standart charmm ff but the total number of errors was bigger than in
case of Swiss params non-standart names usage).

By the way I've simulated choromophore produced by SWISS ( with the
charges assigned from the paper) in the vacuum and didnt notice any
inaccuracy in the conformation of chromophore. So the last that I
should is the carefull assignment of the 9 missed dihedral terms with
the rest of the protein.

James

2012/12/14, Justin Lemkul :
>
>
> On 12/14/12 2:28 PM, James Starlight wrote:
>> Today I've tried to rename atoms from Swiss's params specific names to
>> the standard charmm names and obtain the set of the same errors
>> No default Improper Dih. types
>> No default U-B types
>>   No default Bond types
>>
>>
>> Its strange to me because chromophore itself consist of only one
>> uncommon bond  (in cyclized ring which could produce only several
>> additional angles and dihedrals)
>>
>> By comparison in the case of Swiss atom names the total amount of the
>> same errors was only 9 (all erors about unknown dihedrals with
>> theadjacent residues. Although I've added capes in that model which
>> mimicks adjacent residues) it's difficult recognize suitable dihedral
>> types.
>> Do you know any others attemps to simulate GFP with chromophore in
>> charmm with proof parameters ?
>>
>
> This was linked before, at least once:
>
> http://pubs.acs.org/doi/abs/10.1021/jp014476w
>
> The authors provide parameters for everything you need.  We used these
> several
> years ago.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
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Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

[James Starlight]

The topology with the below params produced that 118 errors during
grompp processings ( after pdb2gmx processing the geoetry of the
mollecule was correct )

[CRN]
 [ atoms ]
CG2  CA-0.0900 0
CD1  CA-0.0800 1
CD2  CA-0.0800 2
CE1  CA-0.2800 3
CE2  CA-0.2800 4
CZ   CA 0.4500 5
NNH1   -0.4700 6
CA1  CPH1   0.1000 7
CB1  CT1   -0.1400 8
CG1  CT30.0900 9
OG1  OH1   -0.6600 10 ;!-0.6800
C1   CPH2   0.5000 11
N2   NR2   -0.6000 12
N3   NR1   -0.5700 13
C2   CPH1   0.5700 14
O3   O -0.5700 15
CA2  CPH1   0.1000 16
CA3  CPH10.1000 17
CC  0.5100 18
OO -0.5100 19
CB2  CE1   -0.1400 20
OH   O -0.6200 21
HA1  HB 0.0700 22
HA32 HB 0.0700 23
HA33 HB 0.0700 24
HD1  HP 0.1400 25
HD2  HP 0.1400 26
HE1  HP 0.1000 27
HE2  HP 0.1000 28
HG11 HA 0.0900 29
HG12 HA 0.0900 30
HG13 HA 0.0900 31
HOG1 H  0.4300 32
HB2  HA10.2100 33
H11  H  0.3700 34
HB1  HA10.2100 36
 [ bonds ]
HG11 CG1
HG12 CG1
CG1  HG13
CG1  CB1
OG1  HOG1
OG1  CB1
CB1  HB1
CB1  CA1
HE2  CE2
NH11
NCA1
CA1  HA1
CA1  C1
CE2  CD2
CE2  CZ
HD2  CD2
OH   CZ
CD2  CG2
CZ   CE1
N2   C1
N2   CA2
C1   N3
HA33 CA3
CG2  CB2
CG2  CD1
CE1  HE1
CE1  CD1
CA2  CB2
CA2  C2
N3   CA3
N3   C2
CB2  HB2
CA3  C
CA3  HA32
CD1  HD1
C2   O3
CO

 [ impropers ]
CG2  CD1  CB2  CD2
CD1  CE1  CG2  HD1
CD2  CE2  CG2  HD2
CE2  CZ   CD2  HE2
CB2  CA2  CG2  HB2
CA2  N2   CB2  C2
C1   CA1  N2   N3
CA1  NC1   CB1
CA1  CB1  C1   HA1
CB1  OG1  CA1  CG1
CB1  CG1  CA1  HB1
C2   N3   CA2  O3
N3   C2   C1   CA3
CA3  CN3   HA33
CA3  HA33 N3   HA32
CZ   CE1  CE2  OH
CE1  CZ   CD1  HE1
CG1  HG11 CB1  HG12
CG1  HG11 CB1  HG13
; with next residue
C+N   CA3  O
; with previous residue
N-C   CA1  H11
[ cmap ]
-C  N  CA1  C1  N2
CA2 C2 N3 CA3 C

The only in that I not sure in that model is the corrections in the
cmap.itp which I added (I've used first two terms which are correspond
to the backbone atoms of the standart amino acid:
C NH1 CT1 C NH1 1 24 24\
C NH1 CT1 C N 1 24 24\
 and renamed it to the chromophore atom names)

by the way If you had had your rtp of the chromophore which you've
done in accordance to that paper could you provide me with them for
comparison with my model ?


James

2012/12/14, Justin Lemkul :
>
>
> On 12/14/12 3:20 PM, James Starlight wrote:
>> Justin,
>>
>> in the case of the system with the atom types assigned from that paper
>> the grompp produced above 118 errors of non standard bond, angle as
>> well as dihedral types ;o So it' seems that some 118 addition terms
>> must be added to the ffbonded.itp to the existing charmm parameters(
>> it's uncommon for me because in that case the atom names werefrom
>> standart charmm ff but the total number of errors was bigger than in
>> case of Swiss params non-standart names usage).
>>
>
> I'm not sure why there were so many errors when you used those parameters.
> Like
> I said, we've used them before.  I recall a few errors along the way, but
> manual
> assignment of the bonded parameters according to the paper is fairly
> straightforward.
>
>> By the way I've simulated choromophore produced by SWISS ( with the
>> charges assigned from the paper) in the vacuum and didnt notice any
>> inaccuracy in the conformation of chromophore. So the last that I
>> should is the carefull assignment of the 9 missed dihedral terms with
>> the rest of the protein.
>>
>
> Sounds like a reasonably approach.  Good luck.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
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