Re: [gmx-users] automating analysis using shell scripting

Hi Hassan, If you have an index file with all the groups, you can use something like: #!/bin/bash groups=`grep ^\[ index.ndx | wc -l` for ((i=0; i$groups; i++)) do echo $((i++)) $i | g_dist ... done This will take groups 0 and 1, 2 and 3, etc, passing the selections to g_dist. If you want

RE: [gmx-users] multiple time step

Hi, Our philosophy up till now is that with bond constraints and hydrogens replaced by virtual sites one can reach a time step of 4 or 5 femtoseconds. This is roughly equal to the largest time step, used for the PME mesh part, in multiple time stepping. But we then do less work on the non-bonded

Re: [gmx-users] ED sampling

Hi Vijaya, could it be that you mixed something up when making the .edi file? The tool make_edi reads the total number of atoms from the provided .tpr file and saves this number with the other ED sampling information to the .edi file. The ED sampling module in mdrun then compares the number

[gmx-users] Dimer g_rms

Dear all, I'm running my first simulation of a dimer. When I run g_rms on Calpha (lsq fit and RMSD calculation on Calpha) to get the RMSD of the whole dimer, the graph is ascending, till reaching a value of 8 A. in this case, I take a .tpr file, a .xtc file and a .ndx file of the whole dimer.

Re: [gmx-users] Dimer g_rms

On Jun 30, 2010, at 10:34 AM, Carla Jamous wrote: Dear all, I'm running my first simulation of a dimer. When I run g_rms on Calpha (lsq fit and RMSD calculation on Calpha) to get the RMSD of the whole dimer, the graph is ascending, till reaching a value of 8 A. in this case, I take a .tpr

[gmx-users] -dt

Hi gromacs users I want to know what is purpose of -dt flag in most of commands? in my analysis, different values for -dt results in outcomes have not determined trend . I used this flag for g_rms as follows : if g_rms -f pr.xtc -s pr.tpr -n pr.ndx-o 5.xvg -dt 5 so : gromacs record

[gmx-users] g_msd and diffusion coefficent

Dear Vitaly Chaban yes. my md simulation is equilibrioum. I did simulation of protein-dna. I want to know how protein and dna close together and interact together (approach of protein to major groove of dna). thanks alot in advance. -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] -dt

Hi, In the mathematical sense, gromacs will only use the frames in the trajectory for which time modulus dt equals 0 (time % dt == 0). Cheers, Tsjerk On Wed, Jun 30, 2010 at 11:47 AM, XAvier Periole x.peri...@rug.nl wrote: -dt will define the frequency of analysis that a program will do. In

[gmx-users] question about Gromacs and Spectroscopy

Hi all, I want to reproduce some experimental data on Spectroscopy using Gromacs. I want to know is it possible? If yes, how to do that? Is there any tutorial related to that? Any help is appreciate! regards, Baofu Qiao -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] the job is not being distributed

Hi, I am using MPICH2 library for gromacs. Thanks and  Regards Syed Tarique Moin -- 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! Please don't post

Re: [gmx-users] question about Gromacs and Spectroscopy

Baofu Qiao wrote: Hi all, I want to reproduce some experimental data on Spectroscopy using Gromacs. I want to know is it possible? If yes, how to do that? Is there any tutorial related to that? Any help is appreciate! Your question is too vague to get much useful advice. The term

[gmx-users] Re: gmx-users Digest, Vol 74, Issue 182

Dear Vitaly Chaban yes. my md simulation is equilibrioum. I did simulation of protein-dna. I want to know how protein and dna close together and interact together (approach of protein to major groove of dna). thanks alot in advance. Dear leila, Please look towards g_rmsdist utility of

[gmx-users] RE: g_msd and diffusion coefficent

Dear Vitaly Chaban yes. my md simulation is equilibrioum. I did simulation of protein-dna. I want to know how protein and dna close together and interact together (approach of protein to major groove of dna). thanks alot in advance. Dear leila, Please look towards g_rmsdist utility of

Re: [gmx-users] Dimer g_rms

XAvier Periole skrev: On Jun 30, 2010, at 10:34 AM, Carla Jamous wrote: Dear all, I'm running my first simulation of a dimer. When I run g_rms on Calpha (lsq fit and RMSD calculation on Calpha) to get the RMSD of the whole dimer, the graph is ascending, till reaching a value of 8 A. in

Re: [gmx-users] question about Gromacs and Spectroscopy

Hi Justin, Thanks for your reply! And sorry for the vague question due to my little knowledge on the spectroscopy. What I want to reproduce is wavenumber of C-H vibrations in alkyl chains. In NMR experiments, such wavenumber is measured to be 2000-3000 cm-1, namely in the middle region of infra

[gmx-users] g_rama / mult

Hi all I used [ g_rama -f *.xtc -s *.tpr -o rama.xvg ] command for analysis of protein. gromacs give me rama.xvg as output but during calculation : Found 68 phi-psi combinations Dihedral around 9,11 not found in topology. Using mult=3 Dihedral around 11,18 not found in topology. Using mult=3

Re: [gmx-users] the job is not being distributed

I think this is not a problem of Gromacs, but the cluster you are using. Try to contact with your cluster administrator, and check the administration software. Syed Tarique Moin wrote: Hi, I am using MPICH2 library for gromacs. Thanks and Regards Syed Tarique Moin --

[gmx-users] b-factor

Hi all pdb file for my protein was obtained by solution NMR. this file is as follows : ATOM 1 N GLY A 1 -25.349 -8.577 4.055 1.00 0.00 ATOM 2 CA GLY A 1 -24.037 -8.099 4.448 1.00 0.00 ATOM 3 C GLY A 1 -23.580 -6.913 3.622 1.00 0.00 ATOM

Re: [gmx-users] b-factor

leila karami skrev: Hi all pdb file for my protein was obtained by solution NMR. this file is as follows : ATOM 1 N GLY A 1 -25.349 -8.577 4.055 1.00 0.00 ATOM 2 CA GLY A 1 -24.037 -8.099 4.448 1.00 0.00 ATOM 3 C GLY A 1 -23.580 -6.913

[gmx-users] multiple dihedrals

Hi all, I'm using ffamber99p ff in gromacs and now I have to use some additional parameters in the force field. Regarding to designation of proper dihedrals in AMBER, in some cases there are 2 or 3 dihedrals given for a specific torsion, in which parameters(e.g. angles) differ from each other 

[gmx-users] Re: gmx-users Digest, Vol 74, Issue 183

? -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100630/aa154dfa/attachment.html -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] Dimer g_rms

On Jun 30, 2010, at 12:47 PM, Erik Marklund wrote: XAvier Periole skrev: On Jun 30, 2010, at 10:34 AM, Carla Jamous wrote: Dear all, I'm running my first simulation of a dimer. When I run g_rms on Calpha (lsq fit and RMSD calculation on Calpha) to get the RMSD of the whole dimer, the

Re: [gmx-users] g_rama / mult

Hi Shahab, I used  [ g_rama -f *.xtc -s *.tpr -o rama.xvg ] command for analysis of Was that your actual command line? If you used a .tpr, why didn't it have all the dihedrals defined then? How did you get it? Anyway, you should be able to assert that the dihedrals mentioned are in fact your

Re: [gmx-users] Dimer g_rms

Hi, Not necessary! If the dimer separates across the boundaries you have a problem of fitting the two together while they are separated. This is only if you use the dimer. The monomers would be fine. That was the case before gromacs 4. But the current versions don't keep molecules whole.

[gmx-users] Re:Chain terminus

Dear All, I had posted here a week or so ago, but fixed my problem, and wanted to post it, and ask if somone has a better method for this: Basically, I have 5 different proteins A-E in a pdb file. I can generate a toplogy initially with pdb2gmx automated, which places the NH3 and COO-

Re: [gmx-users] Dimer g_rms

Thank you for all your replies. Actually, I have already applied trjconv -pbc. So I'm sure that my analysis is on a whole protein, centered in my box. I'm using gromacs 4.0.3 So I think that you were right by saying that my dimer is not stable while my monomers are. But now, I have to fgure out

[gmx-users] g_rama / mult

Dear Tsjerk Wassenaar thanks for your attentions. ok. [ g_rama -f *.xtc -s *.tpr -o rama.xvg ] is my actual command line. I get tpr file by command : grompp -f *.mdp -c *.gro -p *.top -n *.ndx -o *.tpr where I should put multiplicity of 3 (what file) ? -- shahab -- gmx-users

Re: [gmx-users] b-factor

On Wed, 2010-06-30 at 13:07 +0200, Erik Marklund wrote: leila karami skrev: Hi all pdb file for my protein was obtained by solution NMR. this file is as follows : ATOM 1 N GLY A 1 -25.349 -8.577 4.055 1.00 0.00 ATOM 2 CA GLY A 1 -24.037 -8.099

Re: [gmx-users] g_rama / mult

Hi Shahab, The dihedral definitions should be in the .top file. But you don't give any clue to what you've done or what you're doing, so there's nothing more for us to say to try and help you. ok. [ g_rama -f *.xtc -s *.tpr -o rama.xvg ]  is my actual command line. So you're actually using

[gmx-users] residence time of water molecule

Hi how to obtain residence time of water molecule using md simulation and gromacs? What is the best way to do this? Please suggest. -- atila -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] the job is not being distributed

MPICH is known to have problems with GROMACS under at least some circumstances. Try OpenMPI Mark - Original Message - From: Syed Tarique Moin taris...@yahoo.com Date: Wednesday, June 30, 2010 22:36 Subject: [gmx-users] the job is not being distributed To: gmx-users@gromacs.org

Re: [gmx-users] Re: gromacs with CMAP

hi, all Finally figured out that it was because all numbers in the cmap.itp file must be separated by only one space,otherwise the program will read in a zero. I would suggest this to be fixed in the release version. have a nice day. dawei On Tue, Jun 29, 2010 at 9:05 AM, Da-Wei Li

Re: [gmx-users] Re:Chain terminus

- Original Message - From: lloyd riggs lloyd.ri...@gmx.ch Date: Wednesday, June 30, 2010 21:55 Subject: [gmx-users] Re:Chain terminus To: gmx-users@gromacs.org Dear All, I had posted here a week or so ago, but fixed my problem, and wanted to post it, and ask if somone has a

Re: [gmx-users] question about Gromacs and Spectroscopy

- Original Message - From: Baofu Qiao qia...@gmail.com Date: Wednesday, June 30, 2010 20:57 Subject: Re: [gmx-users] question about Gromacs and Spectroscopy To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org Hi Justin, Thanks for your reply! And sorry for

[gmx-users] the job is not being distributed

Hi, Thanks a lot, i will try openmpi. Regards Syed Tarique Moin -- 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! Please don't post (un)subscribe requests

[gmx-users] Pull code

Hi all I am commencing the initial stages for he calculation of potential of mean force of bringing together two cage molecules. I am following the tutorial in such an exercise at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html In contrast to the

Re: [gmx-users] Pull code

Gavin Melaugh wrote: Hi all I am commencing the initial stages for he calculation of potential of mean force of bringing together two cage molecules. I am following the tutorial in such an exercise at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html

[gmx-users] Gromacs to APBS

Dear Gromacs users, I need to determine electric potential on each atom, and I know that APBS has such function. I wanted to first minimize the energies through gromacs and then use the apbs to do the electrostatic calculations. Can you please tell me what file do I need to convert to pqr after

Re: [gmx-users] Pull code

Hi Justin Thanks. If I use the pull_geometry = direction I would go for the following jus t to pull the molecules together in the z direction. pull= umbrella pull_geometry = direction pull_start = yes pull_ngroups = 1 pull_group0 = cage_1 pull_group1 = cage_2 pull_vec1 = 0.0 0.0 -1.0

Re: [gmx-users] Pull code

Gavin Melaugh wrote: Hi Justin Thanks. If I use the pull_geometry = direction I would go for the following jus t to pull the molecules together in the z direction. pull= umbrella pull_geometry = direction pull_start = yes pull_ngroups = 1 pull_group0 = cage_1 pull_group1 = cage_2

[gmx-users] the job is not being distributed

Hello, I have successfully compiled gromacs with openmpi but i see the same problem that the jobs is still not distributed to other nodes but showing all the processor in node and it should be distributed. Thanks and regards Syed Tarique Moin -- gmx-users mailing list

[gmx-users] Overflow problem with test-particle insertion

Hello Gromacs users, I've been doing some simple NVT simulations of Lennard-Jones particles using the built-in 12-6 potential and a tabulated version (vdwtype=user) of this same potential. Both give practically identical results for the density and pressure, but differ in the chemical potential

[gmx-users] index groups

*I read thorough the manual on index groups and creating index file. This is the command I tried: make_ndx -f index.gro -o index.ndx * with index.gro you proposed: [ special ] 1 3 [ all ] 1 2 3 4 error I get: Reading structure file

Re: [gmx-users] index groups

Moeed wrote: *I read thorough the manual on index groups and creating index file. This is the command I tried: make_ndx -f index.gro -o index.ndx * with index.gro you proposed: I posted an index file suitable for use as is. It is not a .gro file. I created the index file using a simple

[gmx-users] Using x2top to convert a gro file to a top file

I have a .gro file and I am trying to convert is to a .top file using x2top. The .gro file is as follows: Octyl Beta Glucoside 48 1OBG O1 2.840 2.397 2.515 1OBG C2 2.938 2.408 2.468 1OBG H3 2.946 2.418 2.356 1OBG C4

[gmx-users] FWSpider Tutorial

Hi I am trying to follow the tutorial listed on http://eugen.leitl.org/chem/kerrigje/pdf_files/fwspidr_tutor.pdf with the latest version of Gromacs, 4.0.7 The commands I typed were pdb2gmx –ignh –ff G43a1 –f 1OMB.pdb –o fws.gro –p fws.top editconf –f fws.gro –d 0.7 editconf –f out.gro –o

Re: [gmx-users] Using x2top to convert a gro file to a top file

Amanda Watkins wrote: I have a .gro file and I am trying to convert is to a .top file using x2top. The .gro file is as follows: Octyl Beta Glucoside 48 1OBG O1 2.840 2.397 2.515 1OBG C2 2.938 2.408 2.468 1OBG H3 2.946 2.418 2.356

Re: [gmx-users] FWSpider Tutorial

Nayef Daher wrote: Hi I am trying to follow the tutorial listed on http://eugen.leitl.org/chem/kerrigje/pdf_files/fwspidr_tutor.pdf with the latest version of Gromacs, 4.0.7 The commands I typed were pdb2gmx –ignh –ff G43a1 –f 1OMB.pdb –o fws.gro –p fws.top editconf –f fws.gro –d 0.7

[gmx-users] Re: using x2top to convert a gro file to a top file

Amanda, X2TOP is a somewhat enigmatic tool. You are never sure when it why it works or refuses to generate a topology... Try to start with PDB file instead of GRO. Try to use -pbc keyword. Try to add new lines to N2T database corresponding to all atoms of your molecule. Good luck, Vitaly I

Re: [gmx-users] Re: using x2top to convert a gro file to a top file

Vitaly Chaban wrote: Amanda, X2TOP is a somewhat enigmatic tool. You are never sure when it why it works or refuses to generate a topology... Try to start with PDB file instead of GRO. Try to use -pbc keyword. Try to add new lines to N2T database corresponding to all atoms of your molecule.

[gmx-users] Re: using x2top to convert a gro file to a top file

Yes, yes... I mixed them up again... One should try that option which is not default. Vitaly Chaban wrote: Amanda, X2TOP is a somewhat enigmatic tool. You are never sure when it why it works or refuses to generate a topology... Try to start with PDB file instead of GRO. Try to use -pbc

Re: [gmx-users] FWSpider Tutorial

Hi Nayef, grompp –f em.mdp –c fws_b4em.gro –p fws.top –o fws_em.tpr genion –s fws_em.tpr –o fws_ion.gro –nname CL- –nn 2 –g fws_ion.log [select Group 12: SOL] pico fws.top [reduce number of SOL by two and add 2 CL- at the end of the file] This is all fine. You take the structure before em,

Re: [gmx-users] the job is not being distributed

Hi Syed, you have to give more information for other people to be able to understand what you are doing. What is the exact sequence of commands you use to start the mdrun job? How does your OpenMPI hostfile look like, how are your nodes called, what does mdrun print on the first lines. Without

Re: [gmx-users] FWSpider Tutorial

Hi Nayef, the next may be useful from technical point of view. if you add the option -p with topology file as an argument to given genion options you don't have to edit the topology file by hand. for example genion –s fws_em.tpr –o fws_ion.gro –nname CL- –nn 2 –g fws_ion.log -p fws.top -pname

Re: [gmx-users] Gromacs to APBS

Hi Vladimir, In [1] there is a option, called Prometheus which allows you to create pqr files from pdb file. Please, see in tools options. I would like to suggest you try to use Prometheus and tell me if it works fine. [1] http://glu.fcfrp.usp.br:8180/prometheus/ Thanks in advance, -- Rodrigo

[gmx-users] Pull code

In addition to what everyone else has said, please note that pull_dim = N N Y is going to allow X and Y distance components to get as large/small as they will without any restraint. This may be what you want, but if you want a distance, but want it to be mostly in Z, then pull_dim = Y Y Y

[gmx-users] Re: gmx-users Digest, Vol 74, Issue 189

Hi Justin I manually modified the fws.top by removing two SOL and adding 2 CL- and that still didn't work. Adding -p flag gave me another type of error, stating that input/output is wrong. I entered the genion command as such genion –s fws_em.tpr –o fws_ion.gro -p fws.top –nname CL- –nn

[gmx-users] Capping residues

Hi, 1) What capping residues are recognized by charmm implemented on gromacs in the latest git version? I was trying to use ACE for acetyl but it is not recognized by pdb2gmx. 2) Is it possible to define caps at residues other than those at the termini? Regards Pooja -- Quaerendo

Re: [gmx-users] Capping residues

Sai Pooja wrote: Hi, 1) What capping residues are recognized by charmm implemented on gromacs in the latest git version? It looks like there aren't any. Check the .rtp file to be sure. I was trying to use ACE for acetyl but it is not recognized by pdb2gmx. 2) Is it possible to define

Re: [gmx-users] Re: gmx-users Digest, Vol 74, Issue 189

Nayef Daher wrote: Hi Justin I manually modified the fws.top by removing two SOL and adding 2 CL- and that still didn't work. Adding -p flag gave me another type of error, stating that input/output is wrong. I entered the genion command as such The actual error message is the only

Re: [gmx-users] Gromacs to APBS

- Original Message - From: Vladimir Lankevich vladimir.lankev...@gmail.com Date: Thursday, July 1, 2010 2:39 Subject: [gmx-users] Gromacs to APBS To: gmx-users@gromacs.org Dear Gromacs users, I need to determine electric potential on each atom, and I know that APBS has such

Re: [gmx-users] the job is not being distributed

- Original Message - From: Syed Tarique Moin taris...@yahoo.com Date: Thursday, July 1, 2010 4:22 Subject: [gmx-users] the job is not being distributed To: gmx-users@gromacs.org --- | Hello, I have successfully compiled gromacs

Re: [gmx-users] Capping residues

- Original Message - From: Justin A. Lemkul jalem...@vt.edu Date: Thursday, July 1, 2010 9:58 Subject: Re: [gmx-users] Capping residues To: Discussion list for GROMACS users gmx-users@gromacs.org Sai Pooja wrote: Hi, 1) What capping residues are recognized by charmm implemented

[gmx-users] amber/charmm force field and HB lifetime at low temperature

Hi gromacs users: Using amber/charmm force field we simulated a solvated protein system at different temperature(300,250 and 200K). I used TIP5P water model and applied NVT ensemble . We analyzed the hydrogen bond life time correlation function(HBCF) to study the protein water interactions.

[gmx-users] protein stability as a dimer

Hello All, I have done simulation for 1ns on a protein dimer using GROMOS96 43a1 force field. I want to study if the protein is stable as  a dimer or not, so can you please give me some suggestion as to what analysis  I could do for the same. I checked g_rms after the simulation, graph which I