Re: [gmx-users] Re: chain ids (2)

[Mark Abraham]

- Original Message -
From: lloyd riggs 
Date: Wednesday, June 23, 2010 15:49
Subject: [gmx-users] Re: chain ids (2)
To: gmx-users@gromacs.org

> 
> Dear All, 
> 
> I am re-posting with some replies to my first message.
> 
> > the cell demensions for .gro files are at the bottomn, 
> 
> you know, you right.  There at the top for .pdb file, and 
> it is just a unit cell, and not very trivial to center 
> graphically. 

Sure, that's one thing editconf is good for.

> And when you answere somones question like below, you should 
> read what they stated first.
> 
> >> I then run an energy minimization in vacuo and it works fine, 
> >>converging in
> >> 800-850 steps at 0.002 ps each
> >>
> 
> >Just FYI, EM is run in steps, not time units.
> 
> I used the term step even?  Correcting every little thing 
> to the point of overdoing it makes people not want to talk to 
> you, especially when it does not solve or answere the 
> problem.  I'm not your dad, you don't have to prove 
> something to me, I know how well you know the software.

When someone asks for help, and appears to demonstrate that they've missed an 
important point (i.e. that time does not elapse during EM), then a helpful tip 
might save them lot of pain at some stage. The person giving the tip isn't 
trying to put anyone down - they're giving their time for free in order to be 
helpful. Criticising the person giving the tip is a great way to dissuade 
others from helping you, too. :-)
 
> In any case, It is obvious my problem is the system blowing up, 
> visually it is only the terminal residues from each chain, and 
> from runs such as lincs warnings, it is the same atoms in these 
> terminal residues, which are the problem.
> 
> Basically, gromacs, as I said, can not keep the chain ids, even 
> when I use an index file, and beforehand, yes I checked all the 
> .itp, .ndx etc to make sure atoms are all properly coordinated.

The chain IDs are irrelevant to GROMACS once pdb2gmx finishes. The information 
encoded by differences in chain ID have been incorporated into the [molecules] 
section.
 
> The extra atoms, I can acount for a couple, such as the extra 
> hydrogen at terminal end, and yes even the interactive use of 
> pdb2gmx as a starting point for the topology still gives 
> problems. 
> 
> Timing wise, it seems to break down when I add waters, when I 
> run this alone, it starts to explode.  I have tried step by 
> step making of .top files as well, and re-adding chain IDs after 
> a crash, etc...or just following a step by step proceedure from 
> scrath again several times.  As I had stated, if the system 
> only has the 5 proteins, and no solvent, it has no problem, but 
> then this is usually the first run after switching from a pdb to 
> .gro file, whith the .pdb generating the .top with it's 
> origional chain IDs.
> 
> SAnd like I said, any helpful suggestions are appriciated.

Justin gave you several - such as providing us with actual pdb2gmx command 
lines. I agree with his guess that you've managed to produce a topology where 
what you intend to be your end-of-chain terminal residues are in fact bound in 
an inter-chain fashion. We can't do more than guess in the absence of actual 
evidence, however.

I do suggest starting afresh in a clean working directory with a version of the 
problem that is as simple as possible  :-)

Mark

> lloyd riggs wrote:
> > Hello again,
> >
> > I am still working on gromacs sims on the side of wet lab 
> work.  In any case,
> > I am still at the same point as almost several weeks back.
> >
> > I can take my pdb file with 5 chain IDs A-C and generate a 
> .top and .gro
> > file, with appropriate box (which can just be pasted at the 
> top of the file I
> > believe) along with the .itps for each chain.
> >
> 
> The box vectors are placed at the *bottom* of a .gro file.  
> Do be careful about
> manually setting a box.  If your coordinates are not 
> positioned appropriately
> and have not been given sufficient solute-box space, then you 
> might see weird
> behavior.  Instead of manually hacking the box, use 
> editconf - that's its purpose.
> 
> > I then run an energy minimization in vacuo and it works fine, 
> converging in
> > 800-850 steps at 0.002 ps each
> >
> 
> Just FYI, EM is run in steps, not time units.
> 
> > I then add waters, and ions (K+, Ca2+, Mg2+, Na+ and Cl-)and 
> generate the
> > larger 37 MB pdb file.
> >
> >> From this, I make_ndx , and additionally specify the residues 
> for each
> >> chain, plus the ions, with Ca2+ in a seperate file (Protein_A-G).
> >
> > Now when I do a simple EM with steep, it say converged in 10-
> 20 cycles, with
> > a rather large force and Potential Energy  =  
> 1.9811578e+20.  When I take
> > just the protein part of the output, I find the terminal 
> residues from each
> > chain try to form a bond (at 10-30 Angstroms away) with the 
> next chein, and
> > from there the system explodes.
> >
> 
> There is no bond formation, that's just a visua

Re: [gmx-users] Problem of reading the atom'force from trr file using template.c

[Mark Abraham]

- Original Message -
From: 聂雪川 
Date: Wednesday, June 23, 2010 18:29
Subject: [gmx-users] Problem of reading the atom'force from trr file using 
template.c
To: gmx-users@gromacs.org

 
---
| 

 
> Dear all,
>I am  trying  to analysis the force of a atom.So I change "fr.x[n][XX]" to 
>  "fr.f[n][XX]" in the template.c .But it turns up "Segmentation fault" .(The  
> pointer "fr.f" is NULL) How could I get the force?

You need to supply a trajectory that has forces, and then make the program read 
the forces (probably with -force on the command line). Alternatively, work 
through how the trajectory reading code works, and see how to set the flags to 
make them read forces.

Mark

 >   > My mdp file: >   > title=   Yo
> cpp  =   /usr/bin/cpp
> constraints  =   all-bonds
> integrator   =   md
> dt   =  0.002 ; ps  !
> nsteps   =  250 ; total 5ns.
> comm_mode =  NonE
> nstcomm  =   
> nstxout  =   50
> nstvout  =   0
> nstfout  =   50
> nstxtcout=   0 
> nstlog   =   5000
> nstenergy=   5000
> nstlist  =   10
> ns_type  =   grid
> coulombtype   =PME
> rlist=   1.4
> rcoulomb =   1.4
> rvdw =   1.4
> pbc  =  xyz
> ; Berendsen temperature coupling is on in two  groups
> Tcoupl   =   berendsen
> tc-grps  =  CNT  SOL 
> tau_t=  0.1 0.1  > ref_t=  300 300 
> ; Energy  monitoring
> energygrps   =  CNT SOL
> ; Non-equilibrium MD >   > freezegrps  = CNP  
> freezedim =  Y Y  Y
> ; Isotropic pressure coupling is now  on
> Pcoupl   =  no
> ;Pcoupltype   =  isotropic
> ;tau_p=  0.5
> ;compressibility =   4.5e-5
> ;ref_p=  1.0
> ; Generate velocites is off at 300  K.
> gen_vel  =   no
> gen_temp =   300.0
> gen_seed =  537129 >   >   > Many thanks in advance,
> Chuan > 
 |
---
 > -- 
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[gmx-users] get the mass having the atom type

[Sebastian Waltz]

Hi all, 

I am using the template.c file to make some individual
analyses. Using top.atoms.atomtype[i] I can get the
information of the atom type of atom i. Is it then possible
to use this information to get the mass of this specific
atom?

Thanks a lot 
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RE: [gmx-users] free energy landscape question

[Kukol, Andreas]

Yes, that is an interesting question. I don't know the answer, but is there any 
way to get the numerical values of the matrix from Gromacs tools that produce a 
matrix in xpm format ? I have problems with g_rms and g_rmsdist is another 
candidate.

Andreas

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> On Behalf Of Andrei Neamtu
> Sent: 23 June 2010 01:00
> To: gmx-users@gromacs.org
> Subject: [gmx-users] free energy landscape question
>
> Hi,
>
> I am trying to use g_sham to obtain free energy landscape from a simulation.
> I can obtain the .xpm files but I want to know if there is any way of
> obtaining the actual histogram (in a form of a ASCII matrix vith
> numerical values) to use it in some other plotting program to draw
> contour lines plots of the surface
>
> Many thanks,
> Andrei
> --
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Re: [gmx-users] free energy landscape question

[Marc F. Lensink]

On Wed, Jun 23, 2010 at 10:20:19AM +0100, Kukol, Andreas wrote:
> Yes, that is an interesting question. I don't know the answer, but is there 
> any way to get the numerical values of the matrix from Gromacs tools that 
> produce a matrix in xpm format ? I have problems with g_rms and g_rmsdist is 
> another candidate.

probably the easiest is to look at the code and print out the matrix
before it's sent to the xpm plotting routine.

you can also convert the xpm afterwards, but I guess the data then
gets quantized.

cheers,
marc
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Re: [gmx-users] get the mass having the atom type

[Mark Abraham]

Sure. Look through the data structures for arrays of mass.

Mark

- Original Message -
From: Sebastian Waltz 
Date: Wednesday, June 23, 2010 19:15
Subject: [gmx-users] get the mass having the atom type
To: gmx-users@gromacs.org

> Hi all, 
> 
> I am using the template.c file to make some individual
> analyses. Using top.atoms.atomtype[i] I can get the
> information of the atom type of atom i. Is it then possible
> to use this information to get the mass of this specific
> atom?
> 
> Thanks a lot 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search 
> before posting!
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Re: [gmx-users] OPLS-AA topologies for ATP

[Thomas Piggot]

Well I would suggest you should do some very careful testing to validate 
the combination of CHARMM charges and one dihedral with the rest of the 
parameters from OPLS. It is not very common (or generally wise) to mix 
and match parameters from different forcefields, see:


http://www.gromacs.org/index.php?title=Documentation/How-tos/Parameterization

I would also say that you should also take care with the OPLS-AA DNA 
parameters as these have not been substantially tested/used and so you 
should double check the atom types for yourself.


On the specific topic of ATP for OPLS-AA/L I have performed simulations 
using the AMBER ATP parameters in OPLS-AA/L (with no changes for 
anything such as the different combination rules) and have found these 
parameters perform just as well as with the AMBER forcefields. There 
will be a section about this (showing the results from some of the tests 
I performed) in a paper I am currently writing.


The AMBER ATP parameters can be found at:

http://www.pharmacy.manchester.ac.uk/bryce/amber#cof

However, I would also ask is there a specific reason you wish to use 
OPLS-AA/L? If not then it is probably easier to use one of the AMBER 
forcefields with these parameters as you do not need to do any testing 
(or wait for me to publish my work!)


Cheers

Tom

BIN ZHANG wrote:
Hi, 

I recently made up a topology for ADP. You can probably modify it to ATP 
easily. 
I used native OPLS atom types based on the DNA parameters 
(http://rnp-group.genebee.msu.su/3d/ff.htm). The charges are copied from 
CHARMM27. Also, there is one dihedral angle missing, again, copied from 
CHARMM.

Please let me know if you have any question, suggestion, 

Cheers,
Bin

===
In the ffoplsaa.rtp file, I added:

[ ADP ]
 [ atoms ]
PBopls_440   1.100 0 ;P
   O1Bopls_441  -0.900 1 ;O
   O2Bopls_441  -0.900 2 ;O
   O3Bopls_441  -0.900 3 ;O
PAopls_440   1.500 4 ;P
   O1Aopls_441  -0.820 5 ;O2
   O2Aopls_441  -0.820 6 ;O2
   O3Aopls_442  -0.740 7 ;OS
   O5'opls_442  -0.620 8 ;OS
   C5'opls_443  -0.080 9 ;CT
  H5''opls_444   0.09010 ;HC
  H5' opls_444   0.09011 ;HC
   C4'opls_158   0.16012 ;CT
   H4'opls_156   0.09013 ;HC
   O4'opls_180  -0.50014 ;OS
   C1'opls_158   0.16015 ;CT
   H1'opls_156   0.09016 ;HC
N9opls_354  -0.05017 ;NA
C8opls_353   0.34018 ;CK
H8opls_359   0.12019 ;H5
N7opls_352  -0.71020 ;NB
C5opls_350   0.28021 ;CB
C6opls_351   0.46022 ;CA
N6opls_356  -0.77023 ;N2
   H61opls_357   0.38024 ;H
   H62opls_358   0.38025 ;H
N1opls_346  -0.74026 ;NC
C2opls_347   0.50027 ;CQ
H2opls_355   0.13028 ;H5
N3opls_348  -0.75029 ;NC
C4opls_349   0.43030 ;CB
   C2'opls_158   0.14031 ;CT
  H2''opls_156   0.09032 ;HC
   O2'opls_171  -0.66033 ;OH
   H2'opls_172   0.43034 ;HO
   C3'opls_158   0.14035 ;CT
   H3'opls_156   0.09036 ;HC
   O3'opls_171  -0.66037 ;OS
   H3Topls_172   0.43038
 [ bonds ]
   PBO3A
   PBO1B
   PBO2B
   PBO3B
  O3A PA
   PAO1A
   PAO2A
   PAO5'
  O3'H3T
  O5'C5'
  C5'C4'
  C4'O4'
  C4'C3'
  O4'C1'
  C1' N9
  C1'C2'
   N9 C4
   N9 C8
   C4 N3
   C2 N1
   C6 N6
   N6H61
   N6H62
   C6 C5
   C5 N7
  C2'C3'
  C2'O2'
  O2'H2'
  C3'O3'
  C1'H1'
  C2'   H2''
  C3'H3'
  C4'H4'
  C5'H5'
  C5'   H5''
   C8 H8
   C2 H2
   N1 C6
   N3 C2
   C4 C5
   N7 C8
===

===
In the ffoplsaabon.itp file, I added:
; copied from ffoplsaanr
[ angletypes ]
  NA CT OS  1   109.500418.680   ; DNA DCY

[ dihedraltypes ]
; these are again copied from ffoplsaanr
  NA  C CM CT  3 30.35430   0.0 -30.35430   
0.0   0.0   0.0 ; aromatic ring DNA DTH
  C  CM CT HC  3 -0.77874  -2.33623   0.0   
3.11498   0.0   0.0 ; aromatic ring DNA DTH 
  HC CT CT NA  3  0.97134   2.91401   0.0 
 -3.88535   0.0   0.0 ; RNA  NA CT CT OH  3 
16.74720 -16.74720   0.0   0.0   0.0   0.0 ; RNA
  CM NA CT OS  3 -3.14010  -3.14010   6.28020   
0.0   0.0   0.0 ; DNA DCY
  C  NA CT OS  3 -3.14010  -3.14010   6.28020   
0.0   0.0   0.0 ; DNA DCY
  CT OS CT NA  3 -5.23350   7.32690   6.28020 
 -8.37360   0.0   0.0 ; 


[ dihedraltypes ]
; copied from charmm
  O2   POS  P  1   0.0   0.12553.0
  O2   POS  P  1   0.0   0.41842.0
  OS   POS  P  1   0.0   0.12553.0
  OS   POS  P  1

Re: [gmx-users] get the mass having the atom type

[Erik Marklund]

Sebastian Waltz skrev:
Hi all, 


I am using the template.c file to make some individual
analyses. Using top.atoms.atomtype[i] I can get the
information of the atom type of atom i. Is it then possible
to use this information to get the mass of this specific
atom?

Thanks a lot 
  

top.atoms.atom[].m

--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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[gmx-users] Re: Problem of reading the atom'force from trr file using template.c

[聂雪川]

Dear Mark ;
The ./template dosn't have additional flags as shows below.The "-force" option 
dosn't work.

==
=Option Filename  Type Description
=
=  -s md.tpr  InputStructure+mass(db): tpr tpb tpa gro g96 pdb
=  -f md.xtc  InputTrajectory: xtc trr trj gro g96 pdb cpt
=
=Option   Type   Value   Description
=--
=-[no]h   bool   no  Print help info and quit
=-niceint0   Set the nicelevel
=-b   time   0   First frame (ps) to read from trajectory
=-e   time   10  Last frame (ps) to read from trajectory
=-dt  time   0   Only use frame when t MOD dt = first time (ps)
=-[no]w   bool   no  View output xvg, xpm, eps and pdb files
=-n   int1   Plot data for atom number n (starting on 1)
===
Chuan

> Date: Wed, 23 Jun 2010 18:40:36 +1000
> From: Mark Abraham 
>  
> You need to supply a trajectory that has forces, and then make the program 
> read the forces (probably with -force on the command line). Alternatively, 
> work through how the trajectory reading code works, and see how to set the 
> flags to make them read forces.
> 
> Mark
> 
> - Original Message -
> From: è,é>ªå· 
> Date: Wednesday, June 23, 2010 18:29
> Subject: [gmx-users] Problem of reading the atom'force from trr file using 
> template.c
> To: gmx-users@gromacs.org
> 
> 
>---
>>> Dear all,
>>I am  trying  to analysis the force of a atom.So I change "fr.x[n][XX]" 
>> to  "fr.f[n][XX]" in the template.c .But it turns up "Segmentation fault" 
>> .(The  pointer "fr.f" is NULL) How could I get the force?
> >   > My mdp file:
 >   > title=   Yo
>> cpp  =   /usr/bin/cpp
>> constraints  =   all-bonds
>> integrator   =   md
>> dt   =  0.002 ; ps  !
>> nsteps   =  250 ; total 5ns.
>> comm_mode =  NonE
>> nstcomm  =   
>> nstxout  =   50
>> nstvout  =   0
>> nstfout  =   50
>> nstxtcout=   0 
>> nstlog   =   5000
>> nstenergy=   5000
>> nstlist  =   10
>> ns_type  =   grid
>> coulombtype   =PME
>> rlist=   1.4
>> rcoulomb =   1.4
>> rvdw =   1.4
>> pbc  =  xyz
>> ; Berendsen temperature coupling is on in two  groups
>> Tcoupl   =   berendsen
>> tc-grps  =  CNT  SOL 
>> tau_t=  0.1 0.1  > ref_t=  300 300 
>> ; Energy  monitoring
>> energygrps   =  CNT SOL
>> ; Non-equilibrium MD >   > freezegrps  = CNP  
>> freezedim =  Y Y  Y
>> ; Isotropic pressure coupling is now  on
>> Pcoupl   =  no
>> ;Pcoupltype   =  isotropic
>> ;tau_p=  0.5
>> ;compressibility =   4.5e-5
>> ;ref_p=  1.0
>> ; Generate velocites is off at 300  K.
>> gen_vel  =   no
>> gen_temp =   300.0
>> gen_seed =  537129 

>   >   > Many thanks in advance,
>> Chuan > 
> |
> ---
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Re: [gmx-users] Re: Problem of reading the atom'force from trr file using template.c

[Sebastian Waltz]

Hi Chuan,

in the template.c file is in the beginning the flag
initialized:

intflags = TRX_READ_X;

If you want to read out the forces you have to change this
to, as:

intflags = TRX_READ_F;

in addition to changing fr.x to fr.f.

Basti 

On Wed, 23 Jun 2010 20:00:27 +0800
 聂雪川  wrote:
> Dear Mark ;
> The ./template dosn't have additional flags as shows
> below.The "-force" option dosn't work.
> 
>
==
> =Option Filename  Type Description
>
=
> =  -s md.tpr  InputStructure+mass(db):
> tpr tpb tpa gro g96 pdb
> =  -f md.xtc  InputTrajectory: xtc trr
> trj gro g96 pdb cpt
> =
> =Option   Type   Value   Description
> =--
> =-[no]h   bool   no  Print help info and quit
> =-niceint0   Set the nicelevel
> =-b   time   0   First frame (ps) to read
> from trajectory
> =-e   time   10  Last frame (ps) to read from
> trajectory
> =-dt  time   0   Only use frame when t MOD dt
> = first time (ps)
> =-[no]w   bool   no  View output xvg, xpm, eps
> and pdb files
> =-n   int1   Plot data for atom number n
> (starting on 1)
>
===
> Chuan
> 
> > Date: Wed, 23 Jun 2010 18:40:36 +1000
> > From: Mark Abraham 
> >  
> > You need to supply a trajectory that has forces, and
> then make the program read the forces (probably with
> -force on the command line). Alternatively, work through
> how the trajectory reading code works, and see how to set
> the flags to make them read forces.
> > 
> > Mark
> > 
> > - Original Message -
> > From: è,é>ªå· 
> > Date: Wednesday, June 23, 2010 18:29
> > Subject: [gmx-users] Problem of reading the atom'force
> from trr file using template.c
> > To: gmx-users@gromacs.org
> > 
> > 
> >
>
   ---
> >>> Dear all,
> >>I am  trying  to analysis the force of a atom.So I
> change "fr.x[n][XX]" to  "fr.f[n][XX]" in the template.c
> .But it turns up "Segmentation fault" .(The  pointer
> "fr.f" is NULL) How could I get the force?
> > >   > My mdp file:
>  >   > title=   Yo
> >> cpp  =   /usr/bin/cpp
> >> constraints  =   all-bonds
> >> integrator   =   md
> >> dt   =  0.002 ; ps  !
> >> nsteps   =  250 ; total 5ns.
> >> comm_mode =  NonE
> >> nstcomm  =   
> >> nstxout  =   50
> >> nstvout  =   0
> >> nstfout  =   50
> >> nstxtcout=   0 
> >> nstlog   =   5000
> >> nstenergy=   5000
> >> nstlist  =   10
> >> ns_type  =   grid
> >> coulombtype   =PME
> >> rlist=   1.4
> >> rcoulomb =   1.4
> >> rvdw =   1.4
> >> pbc  =  xyz
> >> ; Berendsen temperature coupling is on in two  groups
> >> Tcoupl   =   berendsen
> >> tc-grps  =  CNT  SOL 
> >> tau_t=  0.1 0.1  > ref_t
>=  300 300 
> >> ; Energy  monitoring
> >> energygrps   =  CNT SOL
> >> ; Non-equilibrium MD >   > freezegrps  = CNP  
> >> freezedim =  Y Y  Y
> >> ; Isotropic pressure coupling is now  on
> >> Pcoupl   =  no
> >> ;Pcoupltype   =  isotropic
> >> ;tau_p=  0.5
> >> ;compressibility =   4.5e-5
> >> ;ref_p=  1.0
> >> ; Generate velocites is off at 300  K.
> >> gen_vel  =   no
> >> gen_temp =   300.0
> >> gen_seed =  537129 
> 
> >   >   > Many thanks in advance,
> >> Chuan > 
> > |
> >
>
---

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Re: [gmx-users] free energy landscape question

[Andrei Neamtu]

Dear Andreas and Marc,
Thanks for your reply.
I am not familiar with the gromacs programming code and so I am trying
to build myself the FEL.
I can generate the hisotgram of the number of states from the
projection along principal component 1 and 2 (PC1 and PC2) using
SigmaPlot but here I am stucked!

I think that I have to compute the free energy with the formula G = -
kT ln(Pi/Pmax) where Pi is the probability of the state i (determined
py a certain pair of values of PC1 and PC2) and Pmax is the maximum
probability. But for certain there are regions in the principal
component plane with probabiliy zero which constitutes singularities
for the above formula (infinite energy).

Any ideas?

Many thanks,
Andrei

On Wed, Jun 23, 2010 at 12:34 PM, Marc F. Lensink
 wrote:
> On Wed, Jun 23, 2010 at 10:20:19AM +0100, Kukol, Andreas wrote:
>> Yes, that is an interesting question. I don't know the answer, but is there 
>> any way to get the numerical values of the matrix from Gromacs tools that 
>> produce a matrix in xpm format ? I have problems with g_rms and g_rmsdist is 
>> another candidate.
>
> probably the easiest is to look at the code and print out the matrix
> before it's sent to the xpm plotting routine.
>
> you can also convert the xpm afterwards, but I guess the data then
> gets quantized.
>
> cheers,
> marc
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>
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[gmx-users] problem install gromacs in parallel

[Gaurav Goel]

I'm trying to install a local copy of GROMACS on Ohio Super Computer.
I was able to build single and double precision versions (did make
distclean after each), however, got errors while installing parallel
version.

I will appreciate you taking time to help with this installation. Thanks.

This is what I did:

export CPPFLAGS=$FFTW_CFLAGS
export LDFLAGS=$FFTW_LIBS

contents of FFTW_CFLAGS=-I/usr/local/fftw3-3.1.2/include
fftw3.f  fftw3.h

***contents of FFTW_LIBS=-L/usr/local/fftw3-3.1.2/lib -lfftw3 -lfftw3f -lm
libfftw3.alibfftw3f.solibfftw3.lalibfftw3.so.3.1.2
libfftw3f.a   libfftw3f.so.3  libfftw3.sopkgconfig
libfftw3f.la  libfftw3f.so.3.1.2  libfftw3.so.3

***output from './configure --enable-mpi
--prefix=/nfs/18/cwr0350/my_gromacs/gromacs_1_bin
--program-suffix=_mpi &>config.out'

checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking for cc... cc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of cc... gcc3
checking dependency style of cc... gcc3
checking for mpxlc... no
checking for mpicc... mpicc
checking whether the MPI cc command works... yes
checking for catamount... no
checking how to run the C preprocessor... mpicc -E
checking whether mpicc accepts -O3... yes
checking whether mpicc accepts -funroll-all-loops... no
checking whether mpicc accepts -std=gnu99... no
checking whether mpicc accepts  -fast -pc 32 -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused... no
***
* Sorry, these optimization settings don't seem to work for   *
* your C compiler. Use make CFLAGS=..., or edit the top Makefile. *
***
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking whether byte ordering is bigendian... no
checking for int... yes
checking size of int... 4
checking for long int... yes
checking size of long int... 8
checking for long long int... yes
checking size of long long int... 8
checking for off_t... yes
checking size of off_t... 8
checking that size_t can hold pointers... yes
checking floating-point format... IEEE754 (little-endian byte and word order)
checking for a BSD-compatible install... /usr/bin/install -c
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for a sed that does not truncate output... /bin/sed
checking for ld used by mpicc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking how to recognise dependent libraries... pass_all
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from mpicc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if mpicc supports -fno-rtti -fno-exceptions... no
checking for mpicc option to produce PIC... -fPIC
checking if mpicc PIC flag -fPIC works... yes
checking if mpicc static flag -static works... no
checking if mpicc supports -c -o file.o... yes
checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking dynamic linker characteristics... pgcc-Warning-Unknown
switch: -print-search-dirs
/usr/lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports share

[gmx-users] Help in parametrisation

[onetwo]

Hello All,

I am new in this field, and I want to do simulation study on one of the protein 
conatining a metal ion and study its ability to form co-oridnation bond with 
other ligand, which is not defined in GROMOS force field which I have tried. If 
this choice of force field is correct for such type of study ?

I have read Gromacs Manual Chapter 5, also I am following this gromacs mailing 
list for quite some time to get a help on how to include a new metal ion or a 
new ligand in their simulation and they have been refered to refer to the  
http://www.gromacs.org/Documentation/How-tos/Parameterization,

but in this its not mentioned that how to actually do parameterization

neither in manual it has been told on how to generate it ( due apologies,,I 
know, I may be wrong )

and it is more difficult for a person like me who doesnt have much knowledge in 
this field, so if someone can please help me guiding how to do 
parameterisation, I know this is not a trivial task, but still help in this 
regard may help many other fellow users besides me.
Thanks in advance-- 
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Re: [gmx-users] Help in parametrisation

[Justin A. Lemkul]

onetwo wrote:

Hello All,

I am new in this field, and I want to do simulation study on one of the 
protein conatining a metal ion and study its ability to form 
co-oridnation bond with other ligand, which is not defined in GROMOS 
force field which I have tried. If this choice of force field is correct 
for such type of study ?


I have read Gromacs Manual Chapter 5, also I am following this gromacs 
mailing list for quite some time to get a help on how to include a new 
metal ion or a new ligand in their simulation and they have been refered 
to refer to the 
http://www.gromacs.org/Documentation/How-tos/Parameterization,


but in this its not mentioned that how to actually do parameterization

neither in manual it has been told on how to generate it ( due 
apologies,,I know, I may be wrong )




The manual will not cover every possible topic.  Parameterization is described 
in the primary literature for the force field you wish you use.  "GROMOS" is not 
very specific - there are numerous parameter sets within this class of force field.


and it is more difficult for a person like me who doesnt have much 
knowledge in this field, so if someone can please help me guiding how to 
do parameterisation, I know this is not a trivial task, but still help 
in this regard may help many other fellow users besides me.


Aside from telling you to read all the literature you can, there's not much more 
help anyone can do to help you.  You haven't described very well what your 
system is.  What kind of functional groups are in your ligand?  If the 
functional groups are shared with existing parameters, then you'll have a rather 
easy time constructing a topology.  What type of metal ion is it?  If you're 
dealing with a transition metal, using a standard MM force field may not work 
very well.  Note the "Exotic Species" heading on the page you quoted above.


-Justin


Thanks in advance




--


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] OPLS-AA topologies for ATP

[BIN ZHANG]

Dear Tom:

Thanks for your suggestion. You are absolutely right on doing more  
testings. I simply haven't figure out what the appropriate test is  
yet. Could you be more specific about "these parameters perform just  
as well as"? What kind of test did you do?


Also, is there a reason why you choose Amber over Charmm? Is it more  
"compatible" with OPLS?


Thanks,
Bin

On Jun 23, 2010, at 2:48 AM, Thomas Piggot wrote:

Well I would suggest you should do some very careful testing to  
validate the combination of CHARMM charges and one dihedral with the  
rest of the parameters from OPLS. It is not very common (or  
generally wise) to mix and match parameters from different  
forcefields, see:

http://www.gromacs.org/index.php?title=Documentation/How-tos/Parameterization

I would also say that you should also take care with the OPLS-AA DNA  
parameters as these have not been substantially tested/used and so  
you should double check the atom types for yourself.


On the specific topic of ATP for OPLS-AA/L I have performed  
simulations using the AMBER ATP parameters in OPLS-AA/L (with no  
changes for anything such as the different combination rules) and  
have found these parameters perform just as well as with the AMBER  
forcefields. There will be a section about this (showing the results  
from some of the tests I performed) in a paper I am currently writing.


The AMBER ATP parameters can be found at:

http://www.pharmacy.manchester.ac.uk/bryce/amber#cof

However, I would also ask is there a specific reason you wish to use  
OPLS-AA/L? If not then it is probably easier to use one of the AMBER  
forcefields with these parameters as you do not need to do any  
testing (or wait for me to publish my work!)


Cheers

Tom

BIN ZHANG wrote:
Hi, I recently made up a topology for ADP. You can probably modify  
it to ATP easily. I used native OPLS atom types based on the DNA  
parameters (http://rnp-group.genebee.msu.su/3d/ff.htm). The charges  
are copied from CHARMM27. Also, there is one dihedral angle  
missing, again, copied from CHARMM.

Please let me know if you have any question, suggestion, 
Cheers,
Bin
===
In the ffoplsaa.rtp file, I added:
[ ADP ]
[ atoms ]
   PBopls_440   1.100 0 ;P
  O1Bopls_441  -0.900 1 ;O
  O2Bopls_441  -0.900 2 ;O
  O3Bopls_441  -0.900 3 ;O
   PAopls_440   1.500 4 ;P
  O1Aopls_441  -0.820 5 ;O2
  O2Aopls_441  -0.820 6 ;O2
  O3Aopls_442  -0.740 7 ;OS
  O5'opls_442  -0.620 8 ;OS
  C5'opls_443  -0.080 9 ;CT
 H5''opls_444   0.09010 ;HC
 H5' opls_444   0.09011 ;HC
  C4'opls_158   0.16012 ;CT
  H4'opls_156   0.09013 ;HC
  O4'opls_180  -0.50014 ;OS
  C1'opls_158   0.16015 ;CT
  H1'opls_156   0.09016 ;HC
   N9opls_354  -0.05017 ;NA
   C8opls_353   0.34018 ;CK
   H8opls_359   0.12019 ;H5
   N7opls_352  -0.71020 ;NB
   C5opls_350   0.28021 ;CB
   C6opls_351   0.46022 ;CA
   N6opls_356  -0.77023 ;N2
  H61opls_357   0.38024 ;H
  H62opls_358   0.38025 ;H
   N1opls_346  -0.74026 ;NC
   C2opls_347   0.50027 ;CQ
   H2opls_355   0.13028 ;H5
   N3opls_348  -0.75029 ;NC
   C4opls_349   0.43030 ;CB
  C2'opls_158   0.14031 ;CT
 H2''opls_156   0.09032 ;HC
  O2'opls_171  -0.66033 ;OH
  H2'opls_172   0.43034 ;HO
  C3'opls_158   0.14035 ;CT
  H3'opls_156   0.09036 ;HC
  O3'opls_171  -0.66037 ;OS
  H3Topls_172   0.43038
[ bonds ]
  PBO3A
  PBO1B
  PBO2B
  PBO3B
 O3A PA
  PAO1A
  PAO2A
  PAO5'
 O3'H3T
 O5'C5'
 C5'C4'
 C4'O4'
 C4'C3'
 O4'C1'
 C1' N9
 C1'C2'
  N9 C4
  N9 C8
  C4 N3
  C2 N1
  C6 N6
  N6H61
  N6H62
  C6 C5
  C5 N7
 C2'C3'
 C2'O2'
 O2'H2'
 C3'O3'
 C1'H1'
 C2'   H2''
 C3'H3'
 C4'H4'
 C5'H5'
 C5'   H5''
  C8 H8
  C2 H2
  N1 C6
  N3 C2
  C4 C5
  N7 C8
===
===
In the ffoplsaabon.itp file, I added:
; copied from ffoplsaanr
[ angletypes ]
 NA CT OS  1   109.500418.680   ; DNA DCY
[ dihedraltypes ]
; these are again copied from ffoplsaanr
 NA  C CM CT  3 30.35430   0.0 -30.35430
0.0   0.0   0.0 ; aromatic ring DNA DTH
 C  CM CT HC  3 -0.77874  -2.33623   0.0
3.11498   0.0   0.0 ; aromatic ring DNA DTH   HC CT  
CT NA  3  0.97134   2.91401   0.0  -3.88535
0.0   0.0 ; RNA  NA CT CT OH  3  
16.74720 -16.74720   0.0   0.0   0.0   0.0 ; RNA
 CM NA CT OS  3 -3.14010  -3.14010   6.28020
0.0   0.0   0.0 ; DNA DCY
 C  NA CT OS  3 -3.14010  -3.140

[gmx-users] building up a polymer chain

[Moeed]

Hello Justin,

Thanks for your help. Actually, I meant if I use -d option rather than -box
I would have better control on bond distance between monomer units. By try
and error I found out if I used -d 0.0017 the distance between two adjacent
C (2 monomer ends) is 1.54A. which is the bond length for C-C in the
molecule.

editconf -f prodrg.pdb -o prodrgD.gro -d 0.017 -bt cubic

1- To get CH2CH2CH2CH2 repeating unit I removed the H s from both ends by
deleting one of the H at each end of CH3CH2CH2CH3. My chemistry background
is not good, so I wanted to know if the difference in C-H angle and CH2 as a
result of removing the third H in CH3 is negligible. Also the angle between
C atoms at chain ends are not the same as those within the chain. I have
just manupulated the -d option so   |
 |
H
that bond distance is similar to that of C-C on backbone.

I am guessing the answer is by using pdb2gmx the structure file will be
modified so that the mentioned angles are set properly. Please let me know
if I am right and this issue is remediable... How can I make sure this is
not going to affect the simulation given that I am going to build up a very
long chain..


Thanks for your attention.
moeed
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Re: [gmx-users] OPLS-AA topologies for ATP

[Thomas Piggot]

I chose the AMBER ATP for OPLS as I wanted to simulate my system with 
two different all-atom forcefields and knew that I could use AMBER in 
GROMACS with these published parameters (through use of the ffamber 
ports). The only other all-atom forcefield in GROMACS at that time was 
OPLS and rather than attempt a new parameterisation of ATP for OPLS I 
first tried these parameters to see how they would perform.


For the testing then I am sure if you think about this then you can come 
up with some idea's of what good tests would be. If not then look for 
papers where people have done similar things in the past.


Again I must reiterate if you wish to simulate ATP with an all-atom 
forcefield then I would suggest it is currently much easier to use the 
AMBER forcefields than to use OPLS unless there is a specific reason to 
use OPLS.


Cheers

Tom

BIN ZHANG wrote:

Dear Tom:

Thanks for your suggestion. You are absolutely right on doing more
testings. I simply haven't figure out what the appropriate test is
yet. Could you be more specific about "these parameters perform just
as well as"? What kind of test did you do?

Also, is there a reason why you choose Amber over Charmm? Is it more
"compatible" with OPLS?

Thanks,
Bin

On Jun 23, 2010, at 2:48 AM, Thomas Piggot wrote:


Well I would suggest you should do some very careful testing to
validate the combination of CHARMM charges and one dihedral with the
rest of the parameters from OPLS. It is not very common (or
generally wise) to mix and match parameters from different
forcefields, see:
http://www.gromacs.org/index.php?title=Documentation/How-tos/Parameterization

I would also say that you should also take care with the OPLS-AA DNA
parameters as these have not been substantially tested/used and so
you should double check the atom types for yourself.

On the specific topic of ATP for OPLS-AA/L I have performed
simulations using the AMBER ATP parameters in OPLS-AA/L (with no
changes for anything such as the different combination rules) and
have found these parameters perform just as well as with the AMBER
forcefields. There will be a section about this (showing the results
from some of the tests I performed) in a paper I am currently writing.

The AMBER ATP parameters can be found at:

http://www.pharmacy.manchester.ac.uk/bryce/amber#cof

However, I would also ask is there a specific reason you wish to use
OPLS-AA/L? If not then it is probably easier to use one of the AMBER
forcefields with these parameters as you do not need to do any
testing (or wait for me to publish my work!)

Cheers

Tom

BIN ZHANG wrote:

Hi, I recently made up a topology for ADP. You can probably modify
it to ATP easily. I used native OPLS atom types based on the DNA
parameters (http://rnp-group.genebee.msu.su/3d/ff.htm). The charges
are copied from CHARMM27. Also, there is one dihedral angle
missing, again, copied from CHARMM.
Please let me know if you have any question, suggestion, 
Cheers,
Bin
===
In the ffoplsaa.rtp file, I added:
[ ADP ]
[ atoms ]
   PBopls_440   1.100 0 ;P
  O1Bopls_441  -0.900 1 ;O
  O2Bopls_441  -0.900 2 ;O
  O3Bopls_441  -0.900 3 ;O
   PAopls_440   1.500 4 ;P
  O1Aopls_441  -0.820 5 ;O2
  O2Aopls_441  -0.820 6 ;O2
  O3Aopls_442  -0.740 7 ;OS
  O5'opls_442  -0.620 8 ;OS
  C5'opls_443  -0.080 9 ;CT
 H5''opls_444   0.09010 ;HC
 H5' opls_444   0.09011 ;HC
  C4'opls_158   0.16012 ;CT
  H4'opls_156   0.09013 ;HC
  O4'opls_180  -0.50014 ;OS
  C1'opls_158   0.16015 ;CT
  H1'opls_156   0.09016 ;HC
   N9opls_354  -0.05017 ;NA
   C8opls_353   0.34018 ;CK
   H8opls_359   0.12019 ;H5
   N7opls_352  -0.71020 ;NB
   C5opls_350   0.28021 ;CB
   C6opls_351   0.46022 ;CA
   N6opls_356  -0.77023 ;N2
  H61opls_357   0.38024 ;H
  H62opls_358   0.38025 ;H
   N1opls_346  -0.74026 ;NC
   C2opls_347   0.50027 ;CQ
   H2opls_355   0.13028 ;H5
   N3opls_348  -0.75029 ;NC
   C4opls_349   0.43030 ;CB
  C2'opls_158   0.14031 ;CT
 H2''opls_156   0.09032 ;HC
  O2'opls_171  -0.66033 ;OH
  H2'opls_172   0.43034 ;HO
  C3'opls_158   0.14035 ;CT
  H3'opls_156   0.09036 ;HC
  O3'opls_171  -0.66037 ;OS
  H3Topls_172   0.43038
[ bonds ]
  PBO3A
  PBO1B
  PBO2B
  PBO3B
 O3A PA
  PAO1A
  PAO2A
  PAO5'
 O3'H3T
 O5'C5'
 C5'C4'
 C4'O4'
 C4'C3'
 O4'C1'
 C1' N9
 C1'C2'
  N9 C4
  N9 C8
  C4 N3
  C2 N1
  C6 N6
  N6H61
  N6H62
  C6 C5
  C5 N7
 C2'C3'
 C2'O2'
 O2'H2'
 C3'O3'
 C1'H1'
 C2'   H2''
 C3'H3'
 C4'H4'
 C5'H5'
 C5'   H5''
  C8 H8
  C2 H2
  N1 C6
  N3 C2
  C4 C5
  N7 C8
===
=

[gmx-users] Questions about g_sham

[Warren Gallin]

Hi all,

I am trying to use g_sham to generate a free-energy profile based on 
the end-to-end distances of a peptide.

The only documentation that I have been able to find is in the GROMACS 
v.4 pdf manual, which is a little out-of-date, and the g_sham -h output, which 
I assume is the most current.

My input file (dist_div.xvg) is a simple list of distances, one per 
line, stripped out of the g_dist output from a trajectory.

The command line is:

g_sham -f dist_div.xvg -notime -ls Free.xpm -dist energy_dist.xvg -histo 
histogram.xvg -xvgr

The program runs without errors or warnings, but:
1) There is no Free.xpm or histogram.xvg file written
2) The file energy_dist.xvg does not have any of the expected legend code, it 
is only the data for bin number vs. Energy
3) The bin sizes do not seem to be correct i.e. when I divide the difference 
between the largest number and the smallest number by 32, and then check the 
expected boundary values for bin 0 and bin 31, I find lengths in the wrong bins

Can anyone give me some insight into the actual workings of g_sham and 
what I might be doing wrong (or incorrectly expecting) here?

Warren Gallin




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Re: [gmx-users] building up a polymer chain

[Justin A. Lemkul]

Moeed wrote:


Hello Justin,

Thanks for your help. Actually, I meant if I use -d option rather than 
-box I would have better control on bond distance between monomer units. 
By try and error I found out if I used -d 0.0017 the distance between 
two adjacent C (2 monomer ends) is 1.54A. which is the bond length for 
C-C in the molecule.


editconf -f prodrg.pdb -o prodrgD.gro -d 0.017 -bt cubic



There should be no trial and error here.  It is a simple matter of geometry.  As 
long as you've found something that works...


1- To get CH2CH2CH2CH2 repeating unit I removed the H s from both ends 
by deleting one of the H at each end of CH3CH2CH2CH3. My chemistry 
background is not good, so I wanted to know if the difference in C-H 
angle and CH2 as a result of removing the third H in CH3 is negligible. 
Also the angle between C atoms at chain ends are not the same as those 
within the chain. I have just manupulated the -d option so   |
 | 
H

that bond distance is similar to that of C-C on backbone.



All the carbons have sp3 geometry, so I don't see the issue here.

I am guessing the answer is by using pdb2gmx the structure file will be 
modified so that the mentioned angles are set properly. Please let me 
know if I am right and this issue is remediable... How can I make sure 
this is not going to affect the simulation given that I am going to 
build up a very long chain..




If you remove hydrogens and let pdb2gmx build them for you with an appropriate 
.hdb entry, the structure will be fine.  You'll save yourself a lot of time by 
actually doing things instead of waiting for me to tell you what to do.  If you 
encounter a problem, post a question.  Otherwise, the best way to learn is by doing.


-Justin



Thanks for your attention.
moeed



--


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] Questions about g_sham

[Justin A. Lemkul]

Warren Gallin wrote:

Hi all,

I am trying to use g_sham to generate a free-energy profile based on 
the end-to-end distances of a peptide.

The only documentation that I have been able to find is in the GROMACS 
v.4 pdf manual, which is a little out-of-date, and the g_sham -h output, which 
I assume is the most current.

My input file (dist_div.xvg) is a simple list of distances, one per 
line, stripped out of the g_dist output from a trajectory.

The command line is:

g_sham -f dist_div.xvg -notime -ls Free.xpm -dist energy_dist.xvg -histo 
histogram.xvg -xvgr

The program runs without errors or warnings, but:
1) There is no Free.xpm or histogram.xvg file written
2) The file energy_dist.xvg does not have any of the expected legend code, it 
is only the data for bin number vs. Energy
3) The bin sizes do not seem to be correct i.e. when I divide the difference 
between the largest number and the smallest number by 32, and then check the 
expected boundary values for bin 0 and bin 31, I find lengths in the wrong bins

Can anyone give me some insight into the actual workings of g_sham and 
what I might be doing wrong (or incorrectly expecting) here?



Your input file is incorrect.  In order to generate a 2-D free energy surface, 
you need to feed g_sham two variables.  The format of the input .xvg file needs 
to be one of two options:


1. with time

timevalue1  value2

2. without time
value1  value2

The difference can be interpreted by g_sham -[no]time, depending on your 
preference.


-Justin


Warren Gallin






--


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] free energy landscape question

[baptista]

On Wed, 23 Jun 2010, Andrei Neamtu wrote:


Dear Andreas and Marc,
Thanks for your reply.
I am not familiar with the gromacs programming code and so I am trying
to build myself the FEL.
I can generate the hisotgram of the number of states from the
projection along principal component 1 and 2 (PC1 and PC2) using
SigmaPlot but here I am stucked!

I think that I have to compute the free energy with the formula G = -
kT ln(Pi/Pmax) where Pi is the probability of the state i (determined
py a certain pair of values of PC1 and PC2) and Pmax is the maximum
probability. But for certain there are regions in the principal
component plane with probabiliy zero which constitutes singularities
for the above formula (infinite energy).


Hi Andrei,

You can simply assign to those regions a very high energy value (e.g., 
100RT) that works as "+infinite". In practice, this doesn't matter, since 
you will always use an energy cutoff much lower than that when plotting or 
projecting your landscape.


From my experience, you should also pay attention to the choice of bin 
size and the eventual use of smoothing methods, especially if you are 
thinking about going to 3D or higher-dimensional histograms. We ended up 
using kernel density estimates instead of histograms 
(http://dx.doi.org/10.1021/jp902991u).


Have a nice landscaping,
Antonio



Any ideas?

Many thanks,
Andrei

On Wed, Jun 23, 2010 at 12:34 PM, Marc F. Lensink
 wrote:

On Wed, Jun 23, 2010 at 10:20:19AM +0100, Kukol, Andreas wrote:

Yes, that is an interesting question. I don't know the answer, but is there any 
way to get the numerical values of the matrix from Gromacs tools that produce a 
matrix in xpm format ? I have problems with g_rms and g_rmsdist is another 
candidate.


probably the easiest is to look at the code and print out the matrix
before it's sent to the xpm plotting routine.

you can also convert the xpm afterwards, but I guess the data then
gets quantized.

cheers,
marc
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Antonio M. Baptista
Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa
Av. da Republica - EAN
2780-157 Oeiras, Portugal
phone: +351-214469619 email: bapti...@itqb.unl.pt
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Re: [gmx-users] Questions about g_sham

[Warren Gallin]

OK, what if I have only one dimension (end-to-end distance), is there any way 
to do that in GROMACS, or is the best way to just write a little app for myself?

Warren Gallin

On 2010-06-23, at 11:29 AM, Justin A. Lemkul wrote:

> 
> 
> Warren Gallin wrote:
>> Hi all,
>>  I am trying to use g_sham to generate a free-energy profile based on 
>> the end-to-end distances of a peptide.
>>  The only documentation that I have been able to find is in the GROMACS 
>> v.4 pdf manual, which is a little out-of-date, and the g_sham -h output, 
>> which I assume is the most current.
>>  My input file (dist_div.xvg) is a simple list of distances, one per 
>> line, stripped out of the g_dist output from a trajectory.
>> The command line is:
>> g_sham -f dist_div.xvg -notime -ls Free.xpm -dist energy_dist.xvg -histo 
>> histogram.xvg -xvgr
>> The program runs without errors or warnings, but:
>> 1) There is no Free.xpm or histogram.xvg file written
>> 2) The file energy_dist.xvg does not have any of the expected legend code, 
>> it is only the data for bin number vs. Energy
>> 3) The bin sizes do not seem to be correct i.e. when I divide the difference 
>> between the largest number and the smallest number by 32, and then check the 
>> expected boundary values for bin 0 and bin 31, I find lengths in the wrong 
>> bins
>>  Can anyone give me some insight into the actual workings of g_sham and 
>> what I might be doing wrong (or incorrectly expecting) here?
> 
> Your input file is incorrect.  In order to generate a 2-D free energy 
> surface, you need to feed g_sham two variables.  The format of the input .xvg 
> file needs to be one of two options:
> 
> 1. with time
> 
>   timevalue1  value2
> 
> 2. without time
>   value1  value2
> 
> The difference can be interpreted by g_sham -[no]time, depending on your 
> preference.
> 
> -Justin
> 
>> Warren Gallin
>>  
> 
> -- 
> 
> 
> 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/search before posting!
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> 

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Re: [gmx-users] Questions about g_sham

[Justin A. Lemkul]

Warren Gallin wrote:

OK, what if I have only one dimension (end-to-end distance), is there any way 
to do that in GROMACS, or is the best way to just write a little app for myself?


Sounds to me like a problem for PMF, but I seem to recall you had some issues 
with that.  g_sham requires 2 dimensions, so you can't use it for your purposes.


-Justin



Warren Gallin

On 2010-06-23, at 11:29 AM, Justin A. Lemkul wrote:



Warren Gallin wrote:

Hi all,
I am trying to use g_sham to generate a free-energy profile based on 
the end-to-end distances of a peptide.
The only documentation that I have been able to find is in the GROMACS 
v.4 pdf manual, which is a little out-of-date, and the g_sham -h output, which 
I assume is the most current.
My input file (dist_div.xvg) is a simple list of distances, one per 
line, stripped out of the g_dist output from a trajectory.
The command line is:
g_sham -f dist_div.xvg -notime -ls Free.xpm -dist energy_dist.xvg -histo 
histogram.xvg -xvgr
The program runs without errors or warnings, but:
1) There is no Free.xpm or histogram.xvg file written
2) The file energy_dist.xvg does not have any of the expected legend code, it 
is only the data for bin number vs. Energy
3) The bin sizes do not seem to be correct i.e. when I divide the difference 
between the largest number and the smallest number by 32, and then check the 
expected boundary values for bin 0 and bin 31, I find lengths in the wrong bins
Can anyone give me some insight into the actual workings of g_sham and 
what I might be doing wrong (or incorrectly expecting) here?

Your input file is incorrect.  In order to generate a 2-D free energy surface, 
you need to feed g_sham two variables.  The format of the input .xvg file needs 
to be one of two options:

1. with time

timevalue1  value2

2. without time
value1  value2

The difference can be interpreted by g_sham -[no]time, depending on your 
preference.

-Justin


Warren Gallin


--


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] Questions about g_sham

[Warren Gallin]

Justin,

Yes, in order to use the implemented free energy method, the end-to-end 
distance has to be treated like a constraint, creating a closed ring of 
constraints, which on some rare occasions leads to an instability and the 
system blows up.

I think that my best move is to write a little script that creates a 
free energy landscape for 1 dimension only.  Now that I've got g_sham figured 
out, this simple case should be straightforward (he said, invoking the wrath of 
the gods).

Thanks for your insight.

Warren

On 2010-06-23, at 12:03 PM, Justin A. Lemkul wrote:

> Warren Gallin wrote:
>> OK, what if I have only one dimension (end-to-end distance), is there any 
>> way to do that in GROMACS, or is the best way to just write a little app for 
>> myself?
> 
> Sounds to me like a problem for PMF, but I seem to recall you had some issues 
> with that.  g_sham requires 2 dimensions, so you can't use it for your 
> purposes.
> 
> -Justin
> 
> 

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[gmx-users] Position Restrained Simulation for Coarse Grained DSPC

[sunny mishra]

Dear All,

I am trying to run the Position Restrained simulation for the Coarse Grained
DSPC bi-layer. However, I am quite confused that how to generate the
position restraint file for the CG atoms in lipid. Is there a difference
between the position restraint file for the fine grained and coarse grained
structures. Please let me know how to generate the position restraint file
for Coarse Grained DSPC bi-layer. Your reply for the same will be highly
appreciable.

Thanks,

Sunny
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Re: [gmx-users] Position Restrained Simulation for Coarse Grained DSPC

[Justin A. Lemkul]

sunny mishra wrote:

Dear All,

I am trying to run the Position Restrained simulation for the Coarse 
Grained DSPC bi-layer. However, I am quite confused that how to generate 
the position restraint file for the CG atoms in lipid. Is there a 
difference between the position restraint file for the fine grained and 
coarse grained structures. Please let me know how to generate the 
position restraint file for Coarse Grained DSPC bi-layer. Your reply for 
the same will be highly appreciable.


You can generate a position restraint file for any molecule using genrestr. 
Just make sure to supply it with a coordinate file for a single molecule (i.e., 
not your entire bilayer), since position restraints are applied to 
moleculetypes, and not global structures.


-Justin



Thanks,

Sunny



--


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] Position Restrained Simulation for Coarse Grained DSPC

[sunny mishra]

Hi,

Thanks a lot for the quick reply. I want to position restrain the head group
atoms of CG DSPC  but I am not sure about the head group molecules in DSPC.
Can you please tell me how to figure out the head group atoms or molecules.
Also, when you say co-ordinate file then you mean .itp file for the lipid
right?

Thanks

On Wed, Jun 23, 2010 at 2:47 PM, Justin A. Lemkul  wrote:

>
>
> sunny mishra wrote:
>
>> Dear All,
>>
>> I am trying to run the Position Restrained simulation for the Coarse
>> Grained DSPC bi-layer. However, I am quite confused that how to generate the
>> position restraint file for the CG atoms in lipid. Is there a difference
>> between the position restraint file for the fine grained and coarse grained
>> structures. Please let me know how to generate the position restraint file
>> for Coarse Grained DSPC bi-layer. Your reply for the same will be highly
>> appreciable.
>>
>
> You can generate a position restraint file for any molecule using genrestr.
> Just make sure to supply it with a coordinate file for a single molecule
> (i.e., not your entire bilayer), since position restraints are applied to
> moleculetypes, and not global structures.
>
> -Justin
>
>
>> Thanks,
>>
>> Sunny
>>
>>
> --
> 
>
> 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] Position Restrained Simulation for Coarse Grained DSPC

[Justin A. Lemkul]

sunny mishra wrote:

Hi,

Thanks a lot for the quick reply. I want to position restrain the head 
group atoms of CG DSPC  but I am not sure about the head group molecules 
in DSPC. Can you please tell me how to figure out the head group atoms 


Presumably there is a structure of DSPC somewhere you can refer to.  I would 
think you should know the chemical features of the structures they are 
simulating before diving right in blindly :)


or molecules. Also, when you say co-ordinate file then you mean .itp 
file for the lipid right?


No, I mean coordinate file.  An .itp is a topology.

-Justin



Thanks

On Wed, Jun 23, 2010 at 2:47 PM, Justin A. Lemkul > wrote:




sunny mishra wrote:

Dear All,

I am trying to run the Position Restrained simulation for the
Coarse Grained DSPC bi-layer. However, I am quite confused that
how to generate the position restraint file for the CG atoms in
lipid. Is there a difference between the position restraint file
for the fine grained and coarse grained structures. Please let
me know how to generate the position restraint file for Coarse
Grained DSPC bi-layer. Your reply for the same will be highly
appreciable.


You can generate a position restraint file for any molecule using
genrestr. Just make sure to supply it with a coordinate file for a
single molecule (i.e., not your entire bilayer), since position
restraints are applied to moleculetypes, and not global structures.

-Justin


Thanks,

Sunny


-- 



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] free energy landscape question

[Andrei Neamtu]

Dear Antonio,
thank you.
I think I got the idea. I need to use a cut-off for the probability:
for all the probabilities lower than a certain value I assign to them
that (lower) value so the energy will be constant.

Thanks,
Andrei

On Wed, Jun 23, 2010 at 8:49 PM,   wrote:
>
> On Wed, 23 Jun 2010, Andrei Neamtu wrote:
>
>> Dear Andreas and Marc,
>> Thanks for your reply.
>> I am not familiar with the gromacs programming code and so I am trying
>> to build myself the FEL.
>> I can generate the hisotgram of the number of states from the
>> projection along principal component 1 and 2 (PC1 and PC2) using
>> SigmaPlot but here I am stucked!
>>
>> I think that I have to compute the free energy with the formula G = -
>> kT ln(Pi/Pmax) where Pi is the probability of the state i (determined
>> py a certain pair of values of PC1 and PC2) and Pmax is the maximum
>> probability. But for certain there are regions in the principal
>> component plane with probabiliy zero which constitutes singularities
>> for the above formula (infinite energy).
>
> Hi Andrei,
>
> You can simply assign to those regions a very high energy value (e.g.,
> 100RT) that works as "+infinite". In practice, this doesn't matter, since
> you will always use an energy cutoff much lower than that when plotting or
> projecting your landscape.
>
>> From my experience, you should also pay attention to the choice of bin
>
> size and the eventual use of smoothing methods, especially if you are
> thinking about going to 3D or higher-dimensional histograms. We ended up
> using kernel density estimates instead of histograms
> (http://dx.doi.org/10.1021/jp902991u).
>
> Have a nice landscaping,
> Antonio
>
>>
>> Any ideas?
>>
>> Many thanks,
>> Andrei
>>
>> On Wed, Jun 23, 2010 at 12:34 PM, Marc F. Lensink
>>  wrote:
>>>
>>> On Wed, Jun 23, 2010 at 10:20:19AM +0100, Kukol, Andreas wrote:

 Yes, that is an interesting question. I don't know the answer, but is
 there any way to get the numerical values of the matrix from Gromacs tools
 that produce a matrix in xpm format ? I have problems with g_rms and
 g_rmsdist is another candidate.
>>>
>>> probably the easiest is to look at the code and print out the matrix
>>> before it's sent to the xpm plotting routine.
>>>
>>> you can also convert the xpm afterwards, but I guess the data then
>>> gets quantized.
>>>
>>> cheers,
>>> marc
>>> --
>>> gmx-users mailing list    gmx-us...@gromacs.org
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>>
>
> --
> Antonio M. Baptista
> Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa
> Av. da Republica - EAN
> 2780-157 Oeiras, Portugal
> phone: +351-214469619         email: bapti...@itqb.unl.pt
> fax:   +351-214411277         WWW:   http://www.itqb.unl.pt/~baptista
> --
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Re: [gmx-users] grompp fatal error Unknown bond_atomtype

[Peter Huwe]

Thanks for the response, Chris.  And sorry that I was not detailed
enough earlier.  I've read through the manual several times, and I'm
familiar with all of the passages that you cited.  I am parameterizing
PtdIns4,5P2.  OSL is one of the atom types in it (it is a phosphate
ester oxygen).

OSL is in my atomtypes.atp file.

OSL is also in my .rtp file.  I have 6 OSL type atoms (named O1, O13,
OS1, OI1, O4P, & O5P), and each seems to be paired correctly in
accordance the rtp. format.

My problem is that I do not know the origin of the "Fatal error:
Unknown bond_atomtype OSL" error that grompp gave me.  Obviously there
is a problem with one of my files, but which one?  The .atp, the .rtp,
the bon.itp???  I've never received this particular error before. Any
guidance is appreciated.

Thanks,
Peter

On Tue, Jun 22, 2010 at 11:00 PM,   wrote:
> There's lots of information in the gromacs manual to show that the .atp file
> is not the only file that you must modify. My most important suggestion to
> you is that you should read the entire manual, possibly twice, before
> attempting to build new molecules.
>
> Gromacs manual, page 96:
> 5.3.1    Atoms
> A number of static properties are assigned to the atom types in the GROMACS
> force field: Type, Mass, Charge, and ? (see Table 5.2 The mass is listed in
> ff???.atp (see 5.2.1), whereas the charge is listed in ff???.rtp (.rtp =
> residue topology parameter file, see 5.6.1). This implies that the charges
> are only defined in the building blocks of amino acids or user defined
> building blocks. When generating a topology (*.top) using the pdb2gmx
> program the information from these files is combined.
>
> Then on page 97:
> "In the file ff???bon.itp you can add bonded parameters. If you want to
> include parameters for new atom types, make sure you define this new atom
> type in ff???.atp as well."
>
> Then on page 120:
> For each force field there a five files which are only used by pdb2gmx.
> These are: the residue database (.rtp, see 5.6.1) the hydrogen database
> (.hdb, see 5.6.2), two termini databases (.tdb, see 5.6.3) and the atom type
> database (.atp) which contains only the masses.
>
> I'm not going to post a detailed account of how to add an atom because it is
> key for you to fully understand what all of the forcefield files are doing
> if you are going to do something like create a new atom type. The
> information is all in the manual though, and search "exotic species" on the
> wiki, although lots of links there are still broken after the migration to a
> new wiki type.
>
> By the way, you didn't post nearly enough information! You are trying to
> parameterize a new molecule and you got an error and the only thing that you
> posted was the error message . you're much more likely to get good help
> if you make it easier for everybody else to help you.
>
> Chris
>
> -- original message --
>
> Hi Users,
>
> I am experiencing the following fatal error when I try using the
> grompp command.
>
> grompp -f mdout.mdp -r conf.gro -p topol.top
>
> .
> .
> .
> ---
> Program grompp, VERSION 4.0.99-dev-20100409-004
> Source code file: toppush.c, line: 631
>
> Fatal error:
> Unknown bond_atomtype OSL
>
>
> .
> .
> .
> OSL is defined in the atomtypes.atp file located in the force field
> folder that I constructed.  Thus, I do not understand why it is
> "unknown."
>
> Does anybody know how to address this error?
>
> Many Thanks,
> Peter Huwe
>
>
> --
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] grompp fatal error Unknown bond_atomtype

[Justin A. Lemkul]

Are you using the most recent git version?  I think the date string indicates 
you're using a version that's several months old (I could be wrong).  If you 
haven't pulled the latest git, please do.  There have been several changes 
related the the CHARMM implementation and bugs that have been discovered.


-Justin

Peter Huwe wrote:

Thanks for the response, Chris.  And sorry that I was not detailed
enough earlier.  I've read through the manual several times, and I'm
familiar with all of the passages that you cited.  I am parameterizing
PtdIns4,5P2.  OSL is one of the atom types in it (it is a phosphate
ester oxygen).

OSL is in my atomtypes.atp file.

OSL is also in my .rtp file.  I have 6 OSL type atoms (named O1, O13,
OS1, OI1, O4P, & O5P), and each seems to be paired correctly in
accordance the rtp. format.

My problem is that I do not know the origin of the "Fatal error:
Unknown bond_atomtype OSL" error that grompp gave me.  Obviously there
is a problem with one of my files, but which one?  The .atp, the .rtp,
the bon.itp???  I've never received this particular error before. Any
guidance is appreciated.

Thanks,
Peter

On Tue, Jun 22, 2010 at 11:00 PM,   wrote:

There's lots of information in the gromacs manual to show that the .atp file
is not the only file that you must modify. My most important suggestion to
you is that you should read the entire manual, possibly twice, before
attempting to build new molecules.

Gromacs manual, page 96:
5.3.1Atoms
A number of static properties are assigned to the atom types in the GROMACS
force field: Type, Mass, Charge, and ? (see Table 5.2 The mass is listed in
ff???.atp (see 5.2.1), whereas the charge is listed in ff???.rtp (.rtp =
residue topology parameter file, see 5.6.1). This implies that the charges
are only defined in the building blocks of amino acids or user defined
building blocks. When generating a topology (*.top) using the pdb2gmx
program the information from these files is combined.

Then on page 97:
"In the file ff???bon.itp you can add bonded parameters. If you want to
include parameters for new atom types, make sure you define this new atom
type in ff???.atp as well."

Then on page 120:
For each force field there a five files which are only used by pdb2gmx.
These are: the residue database (.rtp, see 5.6.1) the hydrogen database
(.hdb, see 5.6.2), two termini databases (.tdb, see 5.6.3) and the atom type
database (.atp) which contains only the masses.

I'm not going to post a detailed account of how to add an atom because it is
key for you to fully understand what all of the forcefield files are doing
if you are going to do something like create a new atom type. The
information is all in the manual though, and search "exotic species" on the
wiki, although lots of links there are still broken after the migration to a
new wiki type.

By the way, you didn't post nearly enough information! You are trying to
parameterize a new molecule and you got an error and the only thing that you
posted was the error message . you're much more likely to get good help
if you make it easier for everybody else to help you.

Chris

-- original message --

Hi Users,

I am experiencing the following fatal error when I try using the
grompp command.

grompp -f mdout.mdp -r conf.gro -p topol.top

.
.
.
---
Program grompp, VERSION 4.0.99-dev-20100409-004
Source code file: toppush.c, line: 631

Fatal error:
Unknown bond_atomtype OSL


.
.
.
OSL is defined in the atomtypes.atp file located in the force field
folder that I constructed.  Thus, I do not understand why it is
"unknown."

Does anybody know how to address this error?

Many Thanks,
Peter Huwe


--
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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] tutorial on channel simulations

[Sikandar Mashayak]

Hi

I want to perform water channel simulations, where channel is connected to
bath of bulk water at standard thermodynamic conditions. The objective is to
get the density distribution of water inside the channel , which is in
equilibrium with the bath.

Is there any tutorial specific to gromacs which deals with the simulation I
want to perform?

thanks
sikandar
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[gmx-users] Re: gmx-users Digest, Vol 74, Issue 134

[Amin Arabbagheri]

Carsten,

Thanks for your help, I used something like "mpirun -np 3 mdrun -s topol.tpr",
it works but its something like repeating a single job 3 times, simultaneously.
here is the output on the screen :
{
 Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.1#

Back Off! I just backed up ener.edr to ./#ener.edr.1#

Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.2#

Back Off! I just backed up ener.edr to ./#ener.edr.2#

Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.3#

Back Off! I just backed up ener.edr to ./#ener.edr.3#
starting mdrun 'Protein in water'
100 steps,   1000.0 ps.
starting mdrun 'Protein in water'
100 steps,   1000.0 ps.
starting mdrun 'Protein in water'
100 steps,   1000.0 ps.
step 736900, will finish Fri Jun 25 07:45:04 2010
}
the estimated time is as long as one single job!

--- On Mon, 21/6/10, gmx-users-requ...@gromacs.org 
 wrote:

From: gmx-users-requ...@gromacs.org 
Subject: gmx-users Digest, Vol 74, Issue 134
To: gmx-users@gromacs.org
Date: Monday, 21 June, 2010, 9:03

Send gmx-users mailing list submissions to
    gmx-users@gromacs.org

To subscribe or unsubscribe via the World Wide Web, visit
    http://lists.gromacs.org/mailman/listinfo/gmx-users
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of gmx-users digest..."


Today's Topics:

   1. (no subject) (Amin Arabbagheri)
   2. Re: (no subject) (Justin A. Lemkul)
   3. Re: (no subject) (Linus ?stberg)
   4. Re: (no subject) (Carsten Kutzner)
   5. Help with defining new residue (OXY--HEME) (Omololu Akin-Ojo)
   6. Re: Help with defining new residue (OXY--HEME) (Justin A. Lemkul)


--

Message: 1
Date: Mon, 21 Jun 2010 05:00:04 -0700 (PDT)
From: Amin Arabbagheri 
Subject: [gmx-users] (no subject)
To: gmx-users@gromacs.org
Message-ID: <180446.74209...@web50607.mail.re2.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi all,

I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic package 
manager.
I want to run a simulation in parallel on a multi processor, single PC, but to 
compile via grompp, it doesn't accept -np flag, and also , using -np in mdrun, 
it still runs as a single job.
Thanks a lot for any instruction.

Bests,
Amin




      
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Message: 2
Date: Mon, 21 Jun 2010 08:05:15 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] (no subject)
To: Discussion list for GROMACS users 
Message-ID: <4c1f557b.4090...@vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed



Amin Arabbagheri wrote:
> Hi all,
> 
> I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic 
> package manager.
> I want to run a simulation in parallel on a multi processor, single PC, 
> but to compile via grompp, it doesn't accept -np flag, and also , using 
> -np in mdrun, it still runs as a single job.
> Thanks a lot for any instruction.
> 

Regarding grompp:

http://www.gromacs.org/Documentation/FAQs

As for mdrun, please provide your actual command line.  The mdrun -np flag is 
nonfunctional, instead the number of nodes are taken from, i.e. mpirun -np from 
which mdrun is launched.

-Justin

> Bests,
> Amin
> 
> 

-- 


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




--

Message: 3
Date: Mon, 21 Jun 2010 14:07:54 +0200
From: Linus ?stberg 
Subject: Re: [gmx-users] (no subject)
To: Discussion list for GROMACS users 
Message-ID:
    
Content-Type: text/plain; charset="iso-8859-1"

Use grompp normally, without the -np flag. Then run mdrun_mpi with your
normal parameters as mpirun -np x mdrun_mpi -deffnm xx

On Mon, Jun 21, 2010 at 2:00 PM, Amin Arabbagheri wrote:

> Hi all,
>
> I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic
> package manager.
> I want to run a simulation in parallel on a multi processor, single PC, but
> to compile via grompp, it doesn't accept -np flag, and also , using -np in
> mdrun, it still runs as a single job.
> Thanks a lot for any instruction.
>
> Bests,
> Amin
>
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> 

Re: [gmx-users] Help in parametrisation

[onetwo]

Thanks Justin for the help,

I have Manganese in my protein with other two ligands at the active site. 
I am using GROMOS96 43a1 force field.

Mangnese may have topology similar to Magnesium 2+, What I found is that I need 
to do changes in ffG43a1.rtp and ffG43a1nb.itp. But how should I calculate the 
nonbond_params for ffG43a1nb.itp.

For both the other two ligands which contains phosphate and enol groups, I was 
able to create topology using PRODRG server.

Regards

onetwo wrote:
> Hello All,
>
> I am new in this field, and I want to do simulation study on one of the 
> protein conatining a metal ion and study its ability to form co-oridnation 
> bond with other ligand, which is not defined in GROMOS force field which I 
> have tried. If this choice of force field is correct for such type of study ?
>
> I have read Gromacs Manual Chapter 5, also I am following this gromacs 
> mailing list for quite some time to get a help on how to include a new metal 
> ion or a new ligand in their simulation and they have been refered to refer 
> to the http://www.gromacs.org/Documentation/How-tos/Parameterization,
>
> but in this its not mentioned that how to actually do parameterization
>
> neither in manual it has been told on how to generate it ( due apologies,,I 
> know, I may be wrong )
>

The manual will not cover every possible topic.  Parameterization is described 
in the primary literature for the force field you wish you use.  "GROMOS" is 
not very specific - there are numerous parameter sets within this class of 
force field.

> and it is more difficult for a person like me who doesnt have much knowledge 
> in this field, so if someone can please help me guiding how to do 
> parameterisation, I know this is not a trivial task, but still help in this 
> regard may help many other fellow users besides me.

Aside from telling you to read all the literature you can, there's not much 
more help anyone can do to help you.  You haven't described very well what your 
system is.  What kind of functional groups are in your ligand?  If the 
functional groups are shared with existing parameters, then you'll have a 
rather easy time constructing a topology.  What type of metal ion is it?  If 
you're dealing with a transition metal, using a standard MM force field may not 
work very well.  Note the "Exotic Species" heading on the page you quoted above.

-Justin

> Thanks in advance
> 
>

-- 

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] Help in parametrisation

[onetwo]

Thanks Justin for the help,

I have Manganese in my protein with other two ligands at the active site. 
I am using GROMOS96 43a1 force field.

Mangnese may have topology similar to Magnesium 2+, What I found is that I need 
to do changes in ffG43a1.rtp and ffG43a1nb.itp. But how should I calculate the 
nonbond_params for ffG43a1nb.itp.

For both the other two ligands which contains phosphate and enol groups, I was 
able to create topology using PRODRG server.

Regards

onetwo wrote:
> Hello All,
>
> I am new in this field, and I want to do simulation study on one of the 
> protein conatining a metal ion and study its ability to form co-oridnation 
> bond with other ligand, which is not defined in GROMOS force field which I 
> have tried. If this choice of force field is correct for such type of study ?
>
> I have read Gromacs Manual Chapter 5, also I am following this gromacs 
> mailing list for quite some time to get a help on how to include a new metal 
> ion or a new ligand in their simulation and they have been refered to refer 
> to the http://www.gromacs.org/Documentation/How-tos/Parameterization,
>
> but in this its not mentioned that how to actually do parameterization
>
> neither in manual it has been told on how to generate it ( due apologies,,I 
> know, I may be wrong )
>

The manual will not cover every possible topic.  Parameterization is described 
in the primary literature for the force field you wish you use.  "GROMOS" is 
not very specific - there are numerous parameter sets within this class of 
force field.

> and it is more difficult for a person like me who doesnt have much knowledge 
> in this field, so if someone can please help me guiding how to do 
> parameterisation, I know this is not a trivial task, but still help in this 
> regard may help many other fellow users besides me.

Aside from telling you to read all the literature you can, there's not much 
more help anyone can do to help you.  You haven't described very well what your 
system is.  What kind of functional groups are in your ligand?  If the 
functional groups are shared with existing parameters, then you'll have a 
rather easy time constructing a topology.  What type of metal ion is it?  If 
you're dealing with a transition metal, using a standard MM force field may not 
work very well.  Note the "Exotic Species" heading on the page you quoted above.

-Justin

> Thanks in advance
> 
>

-- 

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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