Re: [gmx-users] Simulation of membrane protein

[James Starlight]

Justin,

Could you tell me what difference in inflategro parameters ( cut-off for
lipid removing and scaling factors) should I make for insertion protein in
another bilayes in comparison tu tutorial ?

Now I'm working with DMPC. I've inserted symmetrical alpha helices protein
in this bilayer but inflategro deleate 2 lipid from upper and just 1  from
lower layer. It's strange because I suppose that equal bilayer molecules
would be removed :o


On Inflategro's sites I havenot found such specifity for above parameters
for different bilayers :(

James
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Re: [gmx-users] Re: Problems with g_membed tools

[Wanling Song]

I used the mdp file listed previously to generate the tpr file. It
gave this warning:


WARNING 1 [file membed.mdp]:
  Can not exclude the lattice Coulomb energy between energy groups


then I ignored the warning with -maxwarn 1 and gave the tpr file to
g_membed, command line like this:


  g_membed -f membed.tpr -p topol.top -xyinit 0.1 -xyend 1.0 -nxy 1000


Then it seems the g_membed did one iteration and stopped , it returned this:


Back Off! I just backed up step1b.pdb to ./#step1b.pdb.2#

Back Off! I just backed up step1c.pdb to ./#step1c.pdb.2#
Wrote pdb files with previous and current coordinates
---
Program g_membed, VERSION 4.5.3
Source code file: nsgrid.c, line: 540

Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


I am wondering if it is because the parameters in the mdp file set
improper. How to change it?

Linda



Does this mean that I need to

2011/11/11 Mark Abraham :
> On 11/11/2011 5:13 PM, LindaSong wrote:
>
> Thank you very much for your reply, Mark
>
> It is the topology problem. It seems I did it in a wrong way. Now the
> topology goes like this:
>          [ molecules ]
>  ; Compound    #mols
>     Protein_chain_A  1
>     Protein_chain_A2    1
>     POPC   256
> This problem solved.
>
> But then comes a new one. When I did the g_membed, the system blowed up
> after one iteration!
> I think I really shouldn't ignore the warning from the grompp. However, as
> an inexper ienced user, I don't know how to improve the mdp file. Can you
> give me any hint?
>
> Use a text editor that writes plain text. Junk " " throughout cannot
> help things. As before, reporting the actual text of the warning is critical
> to working out what might be wrong.
>
> Mark
>
> The mdp file for the g_membed is like this:
>
> cpp =  /lib/cpp
> ; Run parameters
> integrator  = md
> nsteps  = 1000
> dt  = 0.002
> ; Output control
> nstxout = 10&n bsp;
> nstvout = 10
> nstenergy   = 10
> nstlog  = 10
> ; Bond parameters
> continuation    = no
> constraint_algorithm = lincs
> constraints = all-bonds
> lincs_iter   = 1
> lincs_order = 4
> ; Neighborsearching
> ns_type = grid
> nstlist = 1
> rlist   = 1.4
> rcoulomb    = 1.4
> rvdw &nb sp;  = 1.4
> ; Electrostatics
> coulombtype = PME
> pme_order   = 4
> fourierspacing  = 0.16
> ; Temperature coupling is on
> tcoupl  = V-rescale
> tc-grps = Protein Non-Protein
> tau_t   = 0.1   0.1   & nbsp;
> ref_t   = 300   300
> ; Pressure coupling is on
> Pcoupl   = Berendsen
> pcoupltype   = semiisotropic
> tau_p    = 1.0
> compressibility  = 4.5e-5  4.5e-5
> ref_p  ;   = 1.0   1.0
> ; Velocity generation
> gen_vel  = yes
> gen_temp = 300
> gen_seed = 173529
> ; Energy monitoring
> energygrps  =  Protein
> ; Non-equilibrium MD
> freezegrps  =  Protein
> freezedim &nb sp; =  Y Y Y
> ; Energy group exclusions
> energygrp_excl  =  Protein Protein
>
> Thanks a lot!
> Linda
>
>
>
>
>
>
>
>
>
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[gmx-users] Charged wall

[Steven Neumann]

Hi Gmx Users,

I am wondering whether is it possible in Gromacs to build sth like a
charged wall to which the last residue of my terminal protein will be
attached and run the simulation? I mean that the protein cannot move
through some border which is attached to and which is positively or
negatively charged.
Thank you

Steven
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[gmx-users] pull_distance

[Алексей Раевский]

hi all.
 I need your advice. I have marked several atoms from one chain and several
atoms from another chain (about 8 from each chain), they are forming  5
h-bonding places, and now I want to stabilize the distance between this
chains during the MD. Can I use com pulling distance Y Y Y for it with
pull_k1 = 2000 and pull_init1 = with pull_rate1 = 0? Will it hold the
initial distance all the time and how many groups I have to create? Will it
be enough 2 groups (one with a selected atoms from first chain and another
with atoms from the second) in the index file or I have to create sveral
groups which will consist of a pairs of groups of atoms involved in
h-bonding? As I understood in this way I will handle a center of mass, so
the first variant is preferable. Is it true?

Thank you for responce

-- 

*

Nemo me impune lacessit*
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Re: [gmx-users] Insertion of the protein into membrane with Gmembed

[Justin A. Lemkul]

James Starlight wrote:

Dear Gromacs Users!



I have some questions about insertion protein into membrane with Gmembed

1) I've used default parameters from gmembed manual for preparing input 
for insertion


integrator = md
energygrp  = Protein
freezegrps = Protein
freezedim  = Y Y Y
energygrp_table
energygrp excl = Protein Protein

Here Protein is my protein group in topology.top


I've obtained 2 warning from gropp

WARNING 1 [file gmembed.mdp, line 27]:
  Unknown left-hand 'energygrp' in parameter file



WARNING 2 [file gmembed.mdp, line 27]:
  Unknown left-hand 'energygrp excl' in parameter file

What does it means ? If I ignore those warnings I've obtain



Both of the warnings indicate typographical errors.  Please see the manual for 
proper keywords.


-Justin

No energy groups defined. This is necessary for energy exclusion in the 
freeze group


May be I should define freezegrps as my lipid group not a protein or use 
ndx file as an alternative ?


Thanks,

James



--


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: mdp file problem

[Justin A. Lemkul]

madhumita das wrote:

Dear Justin,

I could solve that perticular error but another problem has come, After 
running energy minimization, the sulphur and mercury(GG)atoms (present 
in the modified residue of cysteine named CYP at 182 position) break the 
bonds.




Bonds don't break and form during molecular mechanical processes.  Likely 
whatever you're seeing is simply extreme instability in the system.  Most likely 
your topology is wrong.  You haven't said what parameters you're using, but as I 
know I have indicated previously, deriving good parameters for such an exotic 
species will be extremely challenging for the biomolecular force fields present 
in Gromacs.  My guess is that you haven't yet obtained proper parameters.


-Justin

On Thu, Nov 10, 2011 at 7:28 PM, madhumita das 
mailto:madhumita.bioi...@gmail.com>> wrote:


Dear Justin,

I could resolve that perticular error but another problem has come,
After running energy minimization, the sulphur and mercury(GG)atoms
(present in the modified residue of cysteine named CYP at 182
position) break the bonds and become freely moving atoms. I have
attached my prepared gromacs(aqp_newbox) topology(topol.top) and
file obtained after energy mimization(em.gro).
Please help me.
  
Madhumita



On Tue, Nov 8, 2011 at 5:03 PM, madhumita das
mailto:madhumita.bioi...@gmail.com>>
wrote:


Hi GROMACS users,

i am in the midst of simulating  a protein in water.  I have
modified  a residue  in my  pdb file at position  182,  using
amber and then acpype.py.  But  after running  the energy
minimization step,using  em.mdp file  generated from acpype ,
following error comes.

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps= 5000
Step=   17, Dmax= 1.5e-06 nm, Epot=  9.89827e+17 Fmax=
inf, atom= 2700

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 18 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  9.8982703e+17
Maximum force =inf on atom 2700
Norm of force =  1.7474532e+19
 The mdp file is attached.

   Please help.
   
Madhumita Das






--


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] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:

Justin,

Could you tell me what difference in inflategro parameters ( cut-off for 
lipid removing and scaling factors) should I make for insertion protein 
in another bilayes in comparison tu tutorial ?




I've never made any changes; it's always worked just fine.

Now I'm working with DMPC. I've inserted symmetrical alpha helices 
protein in this bilayer but inflategro deleate 2 lipid from upper and 
just 1  from lower layer. It's strange because I suppose that equal 
bilayer molecules would be removed :o




The number of lipids that are removed will depend on the starting configuration 
of the membrane and thus where lipids are relative to the protein. 
Theoretically, a symmetrical protein should delete an equal number of lipids 
from each leaflet, if the geometry of the top and bottom leaflets is comparable. 
 Either try placing the protein at a different location to achieve equivalent 
removal or manually delete a lipid and be sure to equilibrate adequately.




On Inflategro's sites I havenot found such specifity for above 
parameters for different bilayers :(


The cutoffs specified are simple grid search parameters.  They do not 
necessarily need to be altered depending upon the lipid type.


-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] pull_distance

[Justin A. Lemkul]

Алексей Раевский wrote:

hi all.
 I need your advice. I have marked several atoms from one chain and 
several atoms from another chain (about 8 from each chain), they are 
forming  5 h-bonding places, and now I want to stabilize the distance 
between this chains during the MD. Can I use com pulling distance Y Y Y 
for it with pull_k1 = 2000 and pull_init1 = with pull_rate1 = 0? Will it 
hold the initial distance all the time and how many groups I have to 
create? Will it be enough 2 groups (one with a selected atoms from first 
chain and another with atoms from the second) in the index file or I 
have to create sveral groups which will consist of a pairs of groups of 
atoms involved in h-bonding? As I understood in this way I will handle a 
center of mass, so the first variant is preferable. Is it true?
 


Yes.  Create one group for pull_group0, which is the reference (probably 
arbitrary in this case) and another for pull_group1.


-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] Simulation of membrane protein

[James Starlight]

Thanks Justin

I'll try to do that things.

Some addition questions

1) About nvt and apt equilibration

As I understood ref_t of the system  must be equal to temperature of the
phase transition of the specific LIPID.
But in the npt and nvt.mdp files there are severl enties for ref_t ( for
some system groups in index.ndx )
For my system composed of protein dmpc and water :

ref_t   = 323 297323;

Does all this values in mdp file must be equal ( to the temperature of the
lipid  phase transition)
ref_t   = 297 297297

 or each value must correspond to the temperature of phase transition of
the individual element ?
ref_t   = 323 297323;

Does thic correct for both NPT and NVT ensembles ?


James

2011/11/11 Justin A. Lemkul 

>
>
> James Starlight wrote:
>
>> Justin,
>>
>> Could you tell me what difference in inflategro parameters ( cut-off for
>> lipid removing and scaling factors) should I make for insertion protein in
>> another bilayes in comparison tu tutorial ?
>>
>>
> I've never made any changes; it's always worked just fine.
>
>
>  Now I'm working with DMPC. I've inserted symmetrical alpha helices
>> protein in this bilayer but inflategro deleate 2 lipid from upper and just
>> 1  from lower layer. It's strange because I suppose that equal bilayer
>> molecules would be removed :o
>>
>>
> The number of lipids that are removed will depend on the starting
> configuration of the membrane and thus where lipids are relative to the
> protein. Theoretically, a symmetrical protein should delete an equal number
> of lipids from each leaflet, if the geometry of the top and bottom leaflets
> is comparable.  Either try placing the protein at a different location to
> achieve equivalent removal or manually delete a lipid and be sure to
> equilibrate adequately.
>
>
>
>> On Inflategro's sites I havenot found such specifity for above parameters
>> for different bilayers :(
>>
>
> The cutoffs specified are simple grid search parameters.  They do not
> necessarily need to be altered depending upon the lipid type.
>
>
> -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] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:

Thanks Justin

I'll try to do that things.

Some addition questions

1) About nvt and apt equilibration

As I understood ref_t of the system  must be equal to temperature of the 
phase transition of the specific LIPID.
But in the npt and nvt.mdp files there are severl enties for ref_t ( for 
some system groups in index.ndx )

For my system composed of protein dmpc and water :

ref_t   = 323 297323;

Does all this values in mdp file must be equal ( to the temperature of 
the lipid  phase transition)

ref_t   = 297 297297
 
 or each value must correspond to the temperature of phase transition of 
the individual element ?

ref_t   = 323 297323;

Does thic correct for both NPT and NVT ensembles ?



It is incorrect to set different groups at different temperatures.  Whatever 
result you obtain would be completely unrealistic.


-Justin



James

2011/11/11 Justin A. Lemkul mailto:jalem...@vt.edu>>



James Starlight wrote:

Justin,

Could you tell me what difference in inflategro parameters (
cut-off for lipid removing and scaling factors) should I make
for insertion protein in another bilayes in comparison tu tutorial ?


I've never made any changes; it's always worked just fine.


Now I'm working with DMPC. I've inserted symmetrical alpha
helices protein in this bilayer but inflategro deleate 2 lipid
from upper and just 1  from lower layer. It's strange because I
suppose that equal bilayer molecules would be removed :o


The number of lipids that are removed will depend on the starting
configuration of the membrane and thus where lipids are relative to
the protein. Theoretically, a symmetrical protein should delete an
equal number of lipids from each leaflet, if the geometry of the top
and bottom leaflets is comparable.  Either try placing the protein
at a different location to achieve equivalent removal or manually
delete a lipid and be sure to equilibrate adequately.



On Inflategro's sites I havenot found such specifity for above
parameters for different bilayers :(


The cutoffs specified are simple grid search parameters.  They do
not necessarily need to be altered depending upon the lipid type.


-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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--


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] Simulation of membrane protein

[James Starlight]

Justin,

What temperature for NVT phase should be in

gen_temp= 323

Does this parameere must be equal to the ref_t ?

I've obtain strange results after NVT with
ref_t   = 297 297297

for protein in DMPC bilayer.

The bilayer with water parts diffused in up and down direction of the box
relative protein
Why this should occur ? Might I alpy posres for lipid in NVT phase ?

2011/11/11 Justin A. Lemkul 

>
>
> James Starlight wrote:
>
>> Thanks Justin
>>
>> I'll try to do that things.
>>
>> Some addition questions
>>
>> 1) About nvt and apt equilibration
>>
>> As I understood ref_t of the system  must be equal to temperature of the
>> phase transition of the specific LIPID.
>> But in the npt and nvt.mdp files there are severl enties for ref_t ( for
>> some system groups in index.ndx )
>> For my system composed of protein dmpc and water :
>>
>>ref_t   = 323 297323;
>>
>> Does all this values in mdp file must be equal ( to the temperature of
>> the lipid  phase transition)
>> ref_t   = 297 297297
>>  or each value must correspond to the temperature of phase transition of
>> the individual element ?
>>ref_t   = 323 297323;
>>
>> Does thic correct for both NPT and NVT ensembles ?
>>
>>
> It is incorrect to set different groups at different temperatures.
>  Whatever result you obtain would be completely unrealistic.
>
> -Justin
>
>
>> James
>>
>> 2011/11/11 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>
>>
>>
>>
>>James Starlight wrote:
>>
>>Justin,
>>
>>Could you tell me what difference in inflategro parameters (
>>cut-off for lipid removing and scaling factors) should I make
>>for insertion protein in another bilayes in comparison tu tutorial
>> ?
>>
>>
>>I've never made any changes; it's always worked just fine.
>>
>>
>>Now I'm working with DMPC. I've inserted symmetrical alpha
>>helices protein in this bilayer but inflategro deleate 2 lipid
>>from upper and just 1  from lower layer. It's strange because I
>>suppose that equal bilayer molecules would be removed :o
>>
>>
>>The number of lipids that are removed will depend on the starting
>>configuration of the membrane and thus where lipids are relative to
>>the protein. Theoretically, a symmetrical protein should delete an
>>equal number of lipids from each leaflet, if the geometry of the top
>>and bottom leaflets is comparable.  Either try placing the protein
>>at a different location to achieve equivalent removal or manually
>>delete a lipid and be sure to equilibrate adequately.
>>
>>
>>
>>On Inflategro's sites I havenot found such specifity for above
>>parameters for different bilayers :(
>>
>>
>>The cutoffs specified are simple grid search parameters.  They do
>>not necessarily need to be altered depending upon the lipid type.
>>
>>
>>-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
>>
>> 
>> >
>>
>>==**__==
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users
>>
>>
>> 
>> >
>>Please search the archive at
>>
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>>
>>
>> >
>> before posting!
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> --
> ==**==
>
> 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
>
> ==**==

Re: [gmx-users] orca question and LA

[xi zhao]

Dear Sir:
  I want to know version of  groamcs and orca in your the qm/mm 
calculation? are they in parallel ?
thank you!

  



--- 11年11月10日，周四, Micha Ben Achim Kunze  写道：


发件人: Micha Ben Achim Kunze 
主题: Re: [gmx-users] orca question and LA
收件人: gmx-users@gromacs.org
日期: 2011年11月10日,周四,下午7:35



I hope you mean ./configure --with-qmmm-orca --without-qmmm-gaussian etc. 

http://wwwuser.gwdg.de/%7Eggroenh/qmmm.html 
http://www.dddc.ac.cn/embo04/practicals/qmmm/qmmmvacuum.html
www.google.com
etc.

For MPI, I can't really say as I did not get qm/mm with orca/gmx to run in 
parallel yet (using cp2k atm). Maybe someone else can advise you.

Cheers,
Micha


On 10/11/11 10:49, xi zhao wrote: 





I install gmx : ./configure --without-qmmm-orca --without-qmmm-gaussian 
--enable-mpi
  then make 
  make install 
are it right?





--- 11年11月10日，周四, Micha Ben Achim Kunze  写道：


发件人: Micha Ben Achim Kunze 
主题: Re: [gmx-users] orca question and LA
收件人: gmx-users@gromacs.org
日期: 2011年11月10日,周四,下午4:47



Hey there,

my last mail got stuck as it was a bit too large it seems. As I wrote earlier 
there should be NO coordinates in the infofile... It looks like you have a 
problem with gmx not preparing a correct .inp file which should include 
keywords from the infofile, the coordinates of the QMsubsystem and pointcharges 
(depending on the method you use). Are you sure everything is compiled correct 
and that you specified your virtual atoms correctly for your force field (and 
with correct positions/constrains)? Have a look if gmx actually creates an .inp 
file and if yes what it includes.

Again, you should go through Gerrit's tutorials, they should get you going. 
There are also instructions on how to set up LAs for different force fields.

Cheers,
Micha
On 10/11/11 01:19, xi zhao wrote: 






Dear Sir: 
  How to write a correct BASENAME.ORCAINFO file? According to the instruction 
“In the ORCAINFO-file the method, basis set and all other ORCA-specific 
keywords must be given.” It means that BASENAME.ORCAINFO may not contain 
coordinates of QMatoms part, but when groamcs-ORCA runs , it has errors: 
Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp >> pyp_qm.out' 
No atoms to convert in Cartesian2Internal" ; 
When BASENAME.ORCAINFO has coordinates of QMatoms part, ORCA cannot recognizes 
the LA (gromacs dummy atom) in the QMatoms , how to deal with LA , delete LA in 
the BASENAME.ORCAINFO? In fact, the stand-alone version of Orca can normally 
calculates it. Of course, LA must modified! 
  
Kind regards! 
 



 


-下面为附件内容-


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Re: [gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:

Justin,

What temperature for NVT phase should be in

gen_temp= 323

Does this parameere must be equal to the ref_t ?

I've obtain strange results after NVT with
ref_t   = 297 297297


for protein in DMPC bilayer.



You should generate velocities for the temperature you wish to use.  Otherwise, 
equilibration will take longer than necessary.  At worst, it may crash if your 
system is far from equilibrium as the temperature coupling algorithm may fail.


The bilayer with water parts diffused in up and down direction of the 
box relative protein

Why this should occur ? Might I alpy posres for lipid in NVT phase ?



Given that I know nothing about the magnitude of such motion, I can't really 
say.  If there are severe distortions or displacements, restraining headgroup 
atoms may be necessary for the initial phases of equilibration.  Usually such 
restraints should not be necessary for most well-built systems.


-Justin


2011/11/11 Justin A. Lemkul mailto:jalem...@vt.edu>>



James Starlight wrote:

Thanks Justin

I'll try to do that things.

Some addition questions

1) About nvt and apt equilibration

As I understood ref_t of the system  must be equal to
temperature of the phase transition of the specific LIPID.
But in the npt and nvt.mdp files there are severl enties for
ref_t ( for some system groups in index.ndx )
For my system composed of protein dmpc and water :

   ref_t   = 323 297323;

Does all this values in mdp file must be equal ( to the
temperature of the lipid  phase transition)
ref_t   = 297 297297
 or each value must correspond to the temperature of phase
transition of the individual element ?
   ref_t   = 323 297323;

Does thic correct for both NPT and NVT ensembles ?


It is incorrect to set different groups at different temperatures.
 Whatever result you obtain would be completely unrealistic.

-Justin


James

2011/11/11 Justin A. Lemkul mailto:jalem...@vt.edu> >>




   James Starlight wrote:

   Justin,

   Could you tell me what difference in inflategro parameters (
   cut-off for lipid removing and scaling factors) should I make
   for insertion protein in another bilayes in comparison tu
tutorial ?


   I've never made any changes; it's always worked just fine.


   Now I'm working with DMPC. I've inserted symmetrical alpha
   helices protein in this bilayer but inflategro deleate 2
lipid
   from upper and just 1  from lower layer. It's strange
because I
   suppose that equal bilayer molecules would be removed :o


   The number of lipids that are removed will depend on the starting
   configuration of the membrane and thus where lipids are
relative to
   the protein. Theoretically, a symmetrical protein should
delete an
   equal number of lipids from each leaflet, if the geometry of
the top
   and bottom leaflets is comparable.  Either try placing the
protein
   at a different location to achieve equivalent removal or manually
   delete a lipid and be sure to equilibrate adequately.



   On Inflategro's sites I havenot found such specifity for
above
   parameters for different bilayers :(


   The cutoffs specified are simple grid search parameters.  They do
   not necessarily need to be altered depending upon the lipid type.


   -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

   >

   ====
   -- gmx-users mailing listgmx-users@gromacs.org

   >
   http://lists.gromacs.org/mailman/listinfo/gmx-users


   >
   Please search the archive at
   http://www.gr

[gmx-users] Charged wall

[chris . neale]

You could create an atomistic charged wall by placing atoms in a plane  
or grid and using position restraints or freeze groups to keep them in  
place. You could them use the pull code to restrain part of the  
protein relative to an atom(s) in this atomistic wall. You could  
obtain your desired charge distribution by using a combination of  
helium and sodium or chloride atoms. Alternatively, you could create a  
new atom type with a fractional charge and whatever LJ parameters you  
want. Of course, you could also construct a more atomistically  
realistic wall.Some people have done similar things to study proteins  
absorbed onto electrodes:


http://pubs.acs.org/doi/abs/10.1021/ja910707r
http://www.sciencedirect.com/science/article/pii/S0013468609003119

Chris.

-- original message --

Hi Gmx Users,

I am wondering whether is it possible in Gromacs to build sth like a
charged wall to which the last residue of my terminal protein will be
attached and run the simulation? I mean that the protein cannot move
through some border which is attached to and which is positively or
negatively charged.
Thank you

Steven


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[gmx-users] GROMACS/ORCA QMMM

[Jose Tusell]

Dear GROMACS users,

I'm trying to run a QM-MM optimization.  I solvate my protein and add
ions then I do a classical optimization (just GROMACS).  After that I
run grompp with the following minim.mdp file (just showing qmmm
options):

QMMM= yes
QMMM-grps   = Other
QMmethod= RHF
QMbasis = 3-21G
QMMMscheme  = Oniom
QMcharge= -1
QMmult  = 1
SH  = no

This creates the *.tpr file that use to run mdrun.  I use the
following *.ORCAINFO file:

!PAL8 Quick-DFT VerySlowConv
%scf
  Maxiter 300
end
%pal nprocs 8
end

The ORCA run quickly converges but after that mdrun run stops with a
segmentation fault.  Am I missing something in all of this?  Any help
would be greatly appreciated.

Thanks

Jose Tusell
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Re: [gmx-users] Simulation of membrane protein

[James Starlight]

Justin,

It was a huge bilayer replacement on the magnitude comparable with the
protein size. In more detailes both of the lipid leflets moved to the top
and bottom side of the pb. The protein were placed on the old place ( due
to the posres) so it turned out isolated from membrane :)


Also I've found that I could use simulated annealing to slowly warm the
system under *NPT* conditions

So in this case could I skip the nvt phase and do this mod NPT
equilibration ?


also I've create posres for the lipid on Z direction only. I hopes this
helps prevent such bilayer diffusion.

James

2011/11/11 Justin A. Lemkul 

>
>
> James Starlight wrote:
>
>> Justin,
>>
>> What temperature for NVT phase should be in
>>
>> gen_temp= 323
>>
>> Does this parameere must be equal to the ref_t ?
>>
>> I've obtain strange results after NVT with
>> ref_t   = 297 297297
>> for protein in DMPC bilayer.
>>
>>
> You should generate velocities for the temperature you wish to use.
>  Otherwise, equilibration will take longer than necessary.  At worst, it
> may crash if your system is far from equilibrium as the temperature
> coupling algorithm may fail.
>
>
>  The bilayer with water parts diffused in up and down direction of the box
>> relative protein
>> Why this should occur ? Might I alpy posres for lipid in NVT phase ?
>>
>>
> Given that I know nothing about the magnitude of such motion, I can't
> really say.  If there are severe distortions or displacements, restraining
> headgroup atoms may be necessary for the initial phases of equilibration.
>  Usually such restraints should not be necessary for most well-built
> systems.
>
> -Justin
>
>  2011/11/11 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>
>>
>>
>>James Starlight wrote:
>>
>>Thanks Justin
>>
>>I'll try to do that things.
>>
>>Some addition questions
>>
>>1) About nvt and apt equilibration
>>
>>As I understood ref_t of the system  must be equal to
>>temperature of the phase transition of the specific LIPID.
>>But in the npt and nvt.mdp files there are severl enties for
>>ref_t ( for some system groups in index.ndx )
>>For my system composed of protein dmpc and water :
>>
>>   ref_t   = 323 297323;
>>
>>Does all this values in mdp file must be equal ( to the
>>temperature of the lipid  phase transition)
>>ref_t   = 297 297297
>> or each value must correspond to the temperature of phase
>>transition of the individual element ?
>>   ref_t   = 323 297323;
>>
>>Does thic correct for both NPT and NVT ensembles ?
>>
>>
>>It is incorrect to set different groups at different temperatures.
>> Whatever result you obtain would be completely unrealistic.
>>
>>-Justin
>>
>>
>>James
>>
>>2011/11/11 Justin A. Lemkul > >
>>>>
>>
>>
>>
>>
>>   James Starlight wrote:
>>
>>   Justin,
>>
>>   Could you tell me what difference in inflategro parameters (
>>   cut-off for lipid removing and scaling factors) should I
>> make
>>   for insertion protein in another bilayes in comparison tu
>>tutorial ?
>>
>>
>>   I've never made any changes; it's always worked just fine.
>>
>>
>>   Now I'm working with DMPC. I've inserted symmetrical alpha
>>   helices protein in this bilayer but inflategro deleate 2
>>lipid
>>   from upper and just 1  from lower layer. It's strange
>>because I
>>   suppose that equal bilayer molecules would be removed :o
>>
>>
>>   The number of lipids that are removed will depend on the
>> starting
>>   configuration of the membrane and thus where lipids are
>>relative to
>>   the protein. Theoretically, a symmetrical protein should
>>delete an
>>   equal number of lipids from each leaflet, if the geometry of
>>the top
>>   and bottom leaflets is comparable.  Either try placing the
>>protein
>>   at a different location to achieve equivalent removal or
>> manually
>>   delete a lipid and be sure to equilibrate adequately.
>>
>>
>>
>>   On Inflategro's sites I havenot found such specifity for
>>above
>>   parameters for different bilayers :(
>>
>>
>>   The cutoffs specified are simple grid search parameters.  They
>> do
>>   not necessarily need to be altered depending upon the lipid
>> type.
>>
>>
>>   -Justin
>>
>>   -- ==**==
>>
>>
>>
>>   Justin A. Lemkul
>>   Ph.D. Candidate
>>   ICTAS Doctoral Scholar
>>   MILES-IGERT Trainee
>>   Department of Biochemistry
>>   Virginia Tech
>>   Blac

Re: [gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:

Justin,

It was a huge bilayer replacement on the magnitude comparable with the 
protein size. In more detailes both of the lipid leflets moved to the 
top and bottom side of the pb. The protein were placed on the old place 
( due to the posres) so it turned out isolated from membrane :)





If the bilayer is splitting across periodic boundaries (I'm assuming that's what 
you mean by "pb"), then it's more likely that you placed the components of your 
system in an inconvenient way than it is that something is actually wrong.


Also I've found that I could use simulated annealing to slowly warm the 
system under /NPT/ conditions


So in this case could I skip the nvt phase and do this mod NPT 
equilibration ?




Prepare the system in whatever manner is defensible and sensible.  Normally one 
deals with temperature before pressure for stability issues.  If you have found 
a justifiable protocol that leads to a stable simulation, use it.


-Justin



also I've create posres for the lipid on Z direction only. I hopes this 
helps prevent such bilayer diffusion.


James

2011/11/11 Justin A. Lemkul mailto:jalem...@vt.edu>>



James Starlight wrote:

Justin,

What temperature for NVT phase should be in

gen_temp= 323

Does this parameere must be equal to the ref_t ?

I've obtain strange results after NVT with
ref_t   = 297 297297
for protein in DMPC bilayer.



You should generate velocities for the temperature you wish to use.
 Otherwise, equilibration will take longer than necessary.  At
worst, it may crash if your system is far from equilibrium as the
temperature coupling algorithm may fail.


The bilayer with water parts diffused in up and down direction
of the box relative protein
Why this should occur ? Might I alpy posres for lipid in NVT phase ?


Given that I know nothing about the magnitude of such motion, I
can't really say.  If there are severe distortions or displacements,
restraining headgroup atoms may be necessary for the initial phases
of equilibration.  Usually such restraints should not be necessary
for most well-built systems.

-Justin

2011/11/11 Justin A. Lemkul mailto:jalem...@vt.edu> >>



   James Starlight wrote:

   Thanks Justin

   I'll try to do that things.

   Some addition questions

   1) About nvt and apt equilibration

   As I understood ref_t of the system  must be equal to
   temperature of the phase transition of the specific LIPID.
   But in the npt and nvt.mdp files there are severl enties for
   ref_t ( for some system groups in index.ndx )
   For my system composed of protein dmpc and water :

  ref_t   = 323 297323;

   Does all this values in mdp file must be equal ( to the
   temperature of the lipid  phase transition)
   ref_t   = 297 297297
or each value must correspond to the temperature of phase
   transition of the individual element ?
  ref_t   = 323 297323;

   Does thic correct for both NPT and NVT ensembles ?


   It is incorrect to set different groups at different
temperatures.
Whatever result you obtain would be completely unrealistic.

   -Justin


   James

   2011/11/11 Justin A. Lemkul mailto:jalem...@vt.edu>
   >


   

Re: [gmx-users] Simulation of membrane protein

[James Starlight]

Justin,


2011/11/11 Justin A. Lemkul 

>
>
> If the bilayer is splitting across periodic boundaries (I'm assuming
> that's what you mean by "pb"), then it's more likely that you placed the
> components of your system in an inconvenient way than it is that something
> is actually wrong.
>

Bilayer has moved on Z-dimension in periodic box.  That is actually what's
happend :)
http://i1209.photobucket.com/albums/cc394/own11/vmdscene.gif


By the way I'ts intresting that Gmembed has removed 6 lipids in comparison
to the inflateglo ( althought I've done all things in accordance to the
KALP tutorial because my protein is the same).


James
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Re: [gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:

Justin,


2011/11/11 Justin A. Lemkul mailto:jalem...@vt.edu>>



If the bilayer is splitting across periodic boundaries (I'm assuming
that's what you mean by "pb"), then it's more likely that you placed
the components of your system in an inconvenient way than it is that
something is actually wrong.


Bilayer has moved on Z-dimension in periodic box.  That is actually 
what's  happend :)

http://i1209.photobucket.com/albums/cc394/own11/vmdscene.gif



How large of a void exists between your lipids and water prior to starting the 
simulation?  I'm almost certain that you built the unit cell incorrectly - there 
should never be that much free space.




By the way I'ts intresting that Gmembed has removed 6 lipids in 
comparison to the inflateglo ( althought I've done all things in 
accordance to the KALP tutorial because my protein is the same). 



Different algorithms, different results.  Nothing odd about that to me.

-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] Simulation of membrane protein

[James Starlight]

Justin,

The system was compact after inserting protein into bilayer (I've obtain
Area per lipid in accordanc with experimental reference) and futher
minimization (only some llipid tails on the border of the system were
distorded alittle)
But after  nvt simulation this discrepancy occured :)

I've used pbc size like in the KALP simulation because I have bilayer  (
128 lipids) and the protein (38 a.a) of the same size.
My box vectors were 6.500 6.500 6.500

Do you think that I should use smaller pbc? How I could define pbc on the
right size for my purely bilayer system?

I've used

trjconv -s em.tpr -f dmpc128.gro -o dmpc128_whole.gro -pbc mol -ur compact
at the preequilibrated bilayer and than done anything in accordance to
the KALP tutorial


James


2011/11/11 Justin A. Lemkul 

> How large of a void exists between your lipids and water prior to starting
> the simulation?  I'm almost certain that you built the unit cell
> incorrectly - there should never be that much free space.
>
>
>
>> By the way I'ts intresting that Gmembed has removed 6 lipids in
>> comparison to the inflateglo ( althought I've done all things in accordance
>> to the KALP tutorial because my protein is the same).
>>
>
> Different algorithms, different results.  Nothing odd about that to me.
>
> -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
>
> ==**==
> --
> 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.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
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Re: [gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:

Justin,

The system was compact after inserting protein into bilayer (I've obtain 
Area per lipid in accordanc with experimental reference) and futher 
minimization (only some llipid tails on the border of the system were 
distorded alittle)

But after  nvt simulation this discrepancy occured :)

I've used pbc size like in the KALP simulation because I have bilayer  ( 
128 lipids) and the protein (38 a.a) of the same size.


KALP-15 has only 15 residues; your peptide is significantly longer.


My box vectors were 6.500 6.500 6.500

Do you think that I should use smaller pbc? How I could define pbc on 
the right size for my purely bilayer system?




You shouldn't use the box vectors I did in the tutorial - use the dimensions 
present in the actual membrane you're using.  I still see no conceivable way 
that the bilayer separated that much during NVT without significant empty space 
in the unit cell to start.  In NVT, the volume is constant, so if there are 
voids, the lipids will fill to expand them.  I've seen it countless times, so 
please be sure you're actually providing sufficient solvent and an appropriate 
location for all your components within the unit cell.


-Justin


I've used

trjconv -s em.tpr -f dmpc128.gro -o dmpc128_whole.gro -pbc mol -ur compact

at the preequilibrated bilayer and than done anything in accordance to the KALP 
tutorial


James


2011/11/11 Justin A. Lemkul mailto:jalem...@vt.edu>>

How large of a void exists between your lipids and water prior to
starting the simulation?  I'm almost certain that you built the unit
cell incorrectly - there should never be that much free space.



By the way I'ts intresting that Gmembed has removed 6 lipids in
comparison to the inflateglo ( althought I've done all things in
accordance to the KALP tutorial because my protein is the same).


Different algorithms, different results.  Nothing odd about that to me.

-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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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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[gmx-users] g_wham and entropic subtraction

[Sanku M]

Hi,
  I just wanted to check whether g_wham ( in gromacs4.5.4) already subtract the 
entropic contribution ( -2KTlog(r) term ) term when unbiasing the histogram 
obtained from umbrella sampling using distance in 3D as a reaction coordinate.
Thanks
Sanku-- 
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Re: [gmx-users] g_wham and entropic subtraction

[David van der Spoel]

On 2011-11-11 21:29, Sanku M wrote:

Hi,
I just wanted to check whether g_wham ( in gromacs4.5.4) already
subtractthe entropic contribution ( -2KTlog(r) term ) term when
unbiasing the histogram obtained from umbrella sampling using distance
in 3D as a reaction coordinate.
Thanks
Sanku


If it does not say so explicitly (and it does not when using g_wham -h) 
it does not.


--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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[gmx-users] UNK not found in residue topology

[Janowicz, Adrianna C.]

Hello,

I'm getting an UNK not found in residue topology error message.
I figured out what the error was and tried to add carbon to ffopslaa.rtf
but it was unsucessful.

What can I do/How can I change my pdb file from UNK so that Carbon and
Hydrogen can be recognized? (I built my own hydrocarbon strucutre and
added it to an existing PDB file).

Thanks,
Adrianna

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Re: [gmx-users] UNK not found in residue topology

[Justin A. Lemkul]

Janowicz, Adrianna C. wrote:

Hello,

I'm getting an UNK not found in residue topology error message.
I figured out what the error was and tried to add carbon to ffopslaa.rtf
but it was unsucessful.

What can I do/How can I change my pdb file from UNK so that Carbon and
Hydrogen can be recognized? (I built my own hydrocarbon strucutre and
added it to an existing PDB file).



I think you need to be a bit more specific about what you're trying to do.  Are 
you getting errors from pdb2gmx or some other tool?  If so, what are they? 
Otherwise, the only requirement for proper processing is that the PDB format be 
retained and that the atom names match what is expected in the .rtp file.


-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] Positive potential energy for TFE solvent

[Mark Abraham]

On 11/11/2011 5:07 PM, Harpreet Basra wrote:

Hi

I am trying to generate an equilibrated box of 216 TFE molecules.To
generate the 216 TFE molecule box i performed following steps:


A suggested workflow can be found here 
http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation




1) I got the tfe.gro file and created a cubic box of edge length =
0.516 nm containing 1 TFE molecule (at its center), using the
following command:


editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516

  I chose this length because in the tfe.gro file dimensions of the TFE
molecule are 0.516 0.516 0.516.


That's not a good reason. Choose a volume and shape that makes sense for 
your target density. Cubic probably doesn't make sense when a 
rectangular shape is possible. Then you'll probably want to choose -nbox 
differently later.



2) Then using genconf command i replicated the box to get a bigger box
with 216 TFE molecules using the following command:


genconf -f tfe_box.gro  -o out.gro -rot -nbox 6

3) Energy minimization was done using STEEPEST descent

4) Then I performed 5ns NVT (300K) equilibration and followed by 5ns
NPT (300K, 1atm) equilibration.

After doing all these steps still I obtain a positive a potentail
energy. I get positive potential energy of the system (2.45+E04
kJ/mol) and kinetic energy as 4.03+E03 kJ/mol, thus giving a positive
total energy of the system. My question is whether obtaining positive
potential energy indicate some error in my TFE solvent box ? Is it
because of large Fluorine atoms of TFE ? Does it mean its not properly
equilibrated ? What can I do to equilibrate it?


You probably have atomic overlaps from your choice of cubic 0.516 box 
earlier. Did you look at the results of genconf before computing with them?


Mark
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Re: [gmx-users] B-factor to large? Input for TLS

[Henri Mone]

Hi Mark,

Thanks for your reply. I will check if the reference structure and the
trajectory fit.

Cheers
Henrey

On Mon, Nov 7, 2011 at 9:15 PM, Mark Abraham  wrote:
> On 5/11/2011 11:05 AM, Henri Mone wrote:
>>
>> Dear Gromacs Users and Experts,
>>
>> I want to calculate from my xtc trajectory the B-factor and the
>> anisotropic temperature factor.  I'm using following gromacs command:
>>
>> $ g_rmsf -f traj.xtc -o rmsf.xvg -oq bfac.pdb -ox bfac2.pdb -s
>> structure.pdb
>
> Does this reference structure in -s make sense for the trajectory supplied
> for -f? If the computed atomic deviations make no sense, then neither will
> the fluctuations. I have no idea if g_rmsf takes proper account of
> periodicity, but you might need either to massage the trajectory suitably
> with trjconv (see website for suggested workflows), or supply a .tpr with
> the correct box information.
>
>> I want to input the resulting PDB file to the "TLS" Server [1] to
>> calculate the hinge residues for my system.
>> The B-factor which "g_rmsf" is calculating seem to be to large, they
>> are in the range of 2000 to 6000  (last column without the "1.00"
>> prefix) [2].
>> The website [3] suggests that a reasonable  B-factor should is in the
>> range of 21 to 200. Also the TLS server [1] complains that the
>> b-factors are in the wrong range. I did several test but I have no
>> idea what I"m doing wrong. The trajectory is with 250ns long enough to
>> get for my small system a convergence on the B-factor.
>> - I thought it could be a unit problem, what are the B-factor units
>> which "g_rmsf" uses? Could this cause such an huge difference in the
>> b-factor?
>
> g_rmsf converts to Angstroms before writing B-factor output to PDB, as you
> would expect.
>
> Mark
>
>> - What is the standard unit for the b-factor in the PDB definition
>> (from the PDB database)?
>> - What is a realistic range for the b-factor?
>> - What else could be the error source, what am I doing wrong?
>>
>>
>> Thanks, any help is welcome,
>> Henrey
>>
>> ---1: TLSMD SERVER
>> http://skuld.bmsc.washington.edu/~tlsmd/
>>
>>
>>
>> ---2: bfac2.pdb :
>> ...
>> ATOM   6146  N   GLY   435      97.841  52.072  37.712  1.006712.85
>> ATOM   6147  HN  GLY   435      97.972  52.020  37.437  1.006676.79
>> ATOM   6148  CA  GLY   435      97.953  52.003  37.883  1.006739.30
>> ATOM   6149  HA1 GLY   435      97.975  51.822  37.563  1.006956.61
>> ATOM   6150  HA2 GLY   435      97.554  52.041  37.972  1.007042.78
>> ATOM   6151  C   GLY   435      98.601  52.111  38.350  1.006210.20
>> ATOM   6152  O   GLY   435      98.552  51.909  38.905  1.006278.92
>> ATOM   6153  N   ASN   436      99.235  52.437  38.127  1.005772.75
>> ATOM   6154  HN  ASN   436      99.262  52.602  37.668  1.005803.67
>> ATOM   6155  CA  ASN   436      99.904  52.574  38.508  1.005343.12
>> ATOM   6156  HA  ASN   436      99.947  52.400  38.918  1.005671.18
>> ATOM   6157  CB  ASN   436     100.537  52.527  37.948  1.005355.63
>> ATOM   6158  HB1 ASN   436     100.960  52.556  38.127  1.005098.00
>> ATOM   6159  HB2 ASN   436     100.553  52.657  37.601  1.005272.78
>> ATOM   6160  CG  ASN   436     100.587  52.258  37.586  1.006031.62
>> ATOM   6161  OD1 ASN   436     100.582  52.138  37.675  1.006435.18
>> ATOM   6162  ND2 ASN   436     100.641  52.163  37.176  1.006306.09
>> ATOM   6163 1HD2 ASN   436     100.689  51.993  36.928  1.006834.63
>> ATOM   6164 2HD2 ASN   436     100.652  52.264  37.117  1.006062.64
>> ATOM   6165  C   ASN   436      99.947  53.023  38.917  1.004590.56
>> ATOM   6166  O   ASN   436      99.651  53.240  38.597  1.004290.70
>> ...
>>
>> ---3: B-factor range at 3 Å resolution
>> http://www.p212121.com/2009/04/12/b-factor-range-3-resolution/
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[gmx-users] Re: Using CHARMM 36 for DPPC simulation

[Amit Choubey]

Hi Everyone,

I did another simulation where i found the the DPPC area per lipid is 0.61
nm^2 . Is this acceptable ?

I have seen issues like this on the mailing list before can one of the
experts give me some hints.

Amit

On Wed, Nov 9, 2011 at 12:24 PM, Amit Choubey  wrote:

>
> 5Hello all,
>
> I am trying to use CHARMM 36 for DPPC membrane simulation. I did the
> following so far:
>
> 1. Download pdb file containing 128 DPPC molecules from
> http://www.charmm-gui.org/?doc=archive&lib=lipid_pure
>
> 2. I separated one lipid molecule from the obtained pdb file and used
> pdb2gmx -f 1dppc.gro -nochargegrp
>
> The top file obtained was converted to itp file by commenting few things
> out.
>
> 3. I looked at a file named dppc_n128.inp in the downloaded dppc bilayer
> from CHARMM GUI for the box length. I used editconf to convert the pdb to
> gro and manually inserted the box size in the gro file.
>
> 4. Created a system.top file which looks like
> #include "charmm36.ff/forcefield.itp"
> #include "lipid.itp"
> #include "charmm36.ff/tips3p.itp"
>
> [ system ]
> chol
>
> [ molecules ]
> DPPC 128
> SOL  3659
>
> 5. I used following mdp settings
>
> integrator = md ; leap-frog integrator
> nsteps = 2000 ; 40 ns
> dt = 0.002 ; 2 fs
>
> ; Output control
> nstxout = 10 ; save coordinates every 200 ps
> nstvout = 10 ; save velocities every 200 ps
> nstenergy = 1 ; save energies every 2 ps
> nstlog = 1 ; update log file every 2 ps
>
> ; Neighborsearching
> ns_type = grid ; search neighboring grid cels
> nstlist = 10 ; 10 fs
> rlist = 1.0 ; short-range neighborlist cutoff (in nm)
> rlistlong = 1.4
> vdwtype = switch
> rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
> rvdw_switch = 0.8
>
> ; Electrostatics
> rcoulomb= 1.0
> rcoulomb_switch = 0.0
> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
> pme_order = 6 ; cubic interpolation
> fourierspacing = 0.15 ; grid spacing for FFT
>
> ; Temperature coupling is on
> tcoupl = Nose-Hoover ; More accurate thermostat
> tc-grps = DPPC SOL  ; two coupling groups - more accurate
> tau_t = 0.2 0.2 ; time constant, in ps
> ref_t = 323.15 323.15 ; reference temperature, one for each group, in K
>
> ; Pressure coupling is on
> pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
> pcoupltype = semiisotropic ; uniform scaling of x-y box vectors,
> independent z
> tau_p = 5.0 ; time constant, in ps
> ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar)
> compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1
>
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
>
> ; Dispersion correction
> DispCorr = No ; account for cut-off vdW scheme
>
>
> ; Velocity generation
> gen_vel =  yes
> gen_temp=  200.0
> gen_seed=  173529
>
> ; COM motion removal
> nstcomm = 1
> comm-mode   = Linear
> comm-grps   = DPPC SOL
>
> ; Energy monitoring
> energygrps  =  DPPC SOL
>
> ; Bond parameters
> constraint_algorithm = lincs; holonomic constraints
> constraints = hbonds ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter  = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
>
> The resulting simulation gave me an area per lipid =0.591 nm^2. This is
> not quite right. Can somebody suggest what else could i do it get close to
> the 0.63 nm^2 value.
>
> Also when i looked at trajectory file it seemed that the box length was
> not set up quite right because the downloaded pdb file looked ok with the
> membrane in the middle but at the next frame the membrane was at a totally
> different location. The leaflets were separated and the middle of the
> membrane was at the edge of the box.
>
> Also when i used pdb2gmx -nochargegrp on the downloaded file it created a
> gro file whose system size was
>8.20170   8.64120   6.54740 in contrast to6.4   6.4
> 6.38452 .
>
> Amit
>
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Re: [gmx-users] Simulation of membrane protein

[James Starlight]

Justin,


Indeed GenBox added insufficien of the SOL to my system due to the ussage
of increased vdvdat ( I've used 0.350 value for the c atoms only but the
were alot of void beetwen water and bilayer )

lipid_posres in Z directions have prevented the displacement of the bilayer
but the water were distruibuted irregular on the bilayer surface  at the
end of NVT phase

By the way in Gmembed system I have no such problems because the were no
need to use genbox but during processing of the system I've obtain warning

WARNING 1 [file membed.mdp]:
  Can not exclude the lattice Coulomb energy between energy groups



What does it mean?

By the way could I indicate Area per lipid during processing of my system
with the G_membed?


James




2011/11/11 Justin A. Lemkul 

>
>
> James Starlight wrote:
>
>> Justin,
>>
>> The system was compact after inserting protein into bilayer (I've obtain
>> Area per lipid in accordanc with experimental reference) and futher
>> minimization (only some llipid tails on the border of the system were
>> distorded alittle)
>> But after  nvt simulation this discrepancy occured :)
>>
>> I've used pbc size like in the KALP simulation because I have bilayer  (
>> 128 lipids) and the protein (38 a.a) of the same size.
>>
>
> KALP-15 has only 15 residues; your peptide is significantly longer.
>
>
>  My box vectors were 6.500 6.500 6.500
>>
>> Do you think that I should use smaller pbc? How I could define pbc on the
>> right size for my purely bilayer system?
>>
>>
> You shouldn't use the box vectors I did in the tutorial - use the
> dimensions present in the actual membrane you're using.  I still see no
> conceivable way that the bilayer separated that much during NVT without
> significant empty space in the unit cell to start.  In NVT, the volume is
> constant, so if there are voids, the lipids will fill to expand them.  I've
> seen it countless times, so please be sure you're actually providing
> sufficient solvent and an appropriate location for all your components
> within the unit cell.
>
> -Justin
>
>  I've used
>>
>> trjconv -s em.tpr -f dmpc128.gro -o dmpc128_whole.gro -pbc mol -ur compact
>>
>> at the preequilibrated bilayer and than done anything in accordance to
>> the KALP tutorial
>>
>>
>> James
>>
>>
>> 2011/11/11 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>
>>
>>How large of a void exists between your lipids and water prior to
>>starting the simulation?  I'm almost certain that you built the unit
>>cell incorrectly - there should never be that much free space.
>>
>>
>>
>>By the way I'ts intresting that Gmembed has removed 6 lipids in
>>comparison to the inflateglo ( althought I've done all things in
>>accordance to the KALP tutorial because my protein is the same).
>>
>>
>>Different algorithms, different results.  Nothing odd about that to me.
>>
>>-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
>>
>> 
>> >
>>
>>==**__==
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users
>>
>>
>> 
>> >
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>> >
>> before posting!
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>> 
>> >
>>
>>
>>
> --
> ==**==
>
> 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
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs

[gmx-users] picking out resident water molecule?

[Yun Shi]

Hi everyone,

I am doing MD simulation with a protein-ligand system, and I want to pick
out the water molecules (their residue numbers or coordinates in any frame)
that simultaneously contact (within 0.4 nm range for heavy atoms) the
ligand and the protein, so that I could plot the lifetime of these resident
water molecules within a trajectory.

Does anyone know how to achieve this within GROMACS?

Thanks for any advice.
Yun
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