[gmx-users] Re: Calculation of water density around certain protein residues

Hi, I want to know the exact way to calculate the density of water around certain residues in my protein. I tried to calculate this by using g_select, with the following command :- g_select -f nvt.trr -s nvt.tpr -select Nearby water resname SOL and within 0.5 of resnr 115 to 118 -os water.xvg

[gmx-users] Different Residues...

Hello Dear GROMACS users, I trying to do a MD calculation using GROMACS, but when I running pdb2gmx I get the following error: Fatal error: Residue '' not found in residue topology database I'm a beginner GROMACS user, but I want to know exactly, how add my residues to GROMACS step by step?.

[gmx-users] Fw: energy minimization problem

Dear Justin  Further to your previous email, I want to calculate free energy for DNA-ligand interaction. According to your answer, for more sensitive calculations like free energy simulations and normal modes, emtol should be lower than 1. As I  understand, you mean that for these systems emtol

Re: [gmx-users] TFE-water simulation

Hello Archana, I'm also toying with a TFE-water system, therefore I am also a newbie. This is what I am doing, I hope it helps: 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I don't use PRODGR, see why in DOI: 10.1021/ci100335w). 2) Do the math and check how many

Re: [gmx-users] Gromacs-4.6 on two Titans GPUs

That should be enough. You may want to use the -march (or equivalent) compiler flag for CPU optimization. Cheers, -- Szilárd Páll On Sun, Nov 3, 2013 at 10:01 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs Users! I'd like to compile lattest 4.6 Gromacs with native GPU

[gmx-users] gmxcheck

Hi, I was wondering if anyone could help me with the gmxcheck function? In the manual it is written, -m flag is given a LaTeX file will be written consisting of a rough outline for a methods section for a paper. I tried it several times but there isn't any file that I can see. I had run some

Re: [gmx-users] TFE-water simulation

Erratum: Where I wrote I ended up going with the former it should be I ended up going with the latter. /J On Mon, Nov 4, 2013 at 10:47 AM, João Henriques joao.henriques.32...@gmail.com wrote: Hello Archana, I'm also toying with a TFE-water system, therefore I am also a newbie. This is

[gmx-users] Re: Installation Gromacs 4.5.7 on rocluster cluster with centos 6.0

Hi, I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works fine till .configure command, but I am getting error at the make command :- Error: [root@cluster gromacs-4.5.7]# make /bin/sh ./config.status --recheck running CONFIG_SHELL=/bin/sh /bin/sh

[gmx-users] Wall potential for a membrane simulation

Hello, I would like to simulate a membrane system with two walls, one at the bottom of my box at z=0 and one at the top, using the gromos53a6 forcefield (GROMACS version 4.5.5). My testing system consists of a membrane in the middle, water and sodium ions (40xNa+) above the membrane and water

[gmx-users] Calculation of water density around certain protein residues

Hi, I want to know the exact way to calculate the density of water around certain residues in my protein. I tried to calculate this by using g_select, with the following command :- g_select -f nvt.trr -s nvt.tpr -select Nearby water resname SOL and within 0.5 of resnr 115 to 118 -os water.xvg

[gmx-users] Fwd: Installation Gromacs 4.5.7 on rocluster cluster with centos 6.0

Hi, I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works fine till .configure command, but I am getting error at the make command :- Error: [root@cluster gromacs-4.5.7]# make /bin/sh ./config.status --recheck running CONFIG_SHELL=/bin/sh /bin/sh

Re: [gmx-users] Gromacs-4.6 on two Titans GPUs

Szilárd, thanks for suggestion! What kind of CPU optimisation should I take into account assumint that I'm using dual-GPU Nvidia TITAN workstation with 6 cores i7 (recognized as 12 nodes in Debian). James 2013/11/4 Szilárd Páll pall.szil...@gmail.com That should be enough. You may want to

Re: [gmx-users] DPOSRES and energy minimization

On 11/4/13 1:31 AM, Gianluca Interlandi wrote: Is there a way to tell from the log file whether positional restraints are really activated or not? Yes, there is a position restraint energy term written to the .log and .edr files if the restraints are active. -Justin --

Re: [gmx-users] g_lie useage

On 11/4/13 1:52 AM, Saman Shahriyari wrote: dear gmx users i am trying to use g_lie tool regarding the fact i am a newbie to this. so i searched through the web for an appropriate protocol. although there are lots of staffs discussing the theory, but i couldn't find any thing describing

Re: [gmx-users] Different Residues...

On 11/4/13 3:16 AM, Ramon Valencia wrote: Hello Dear GROMACS users, I trying to do a MD calculation using GROMACS, but when I running pdb2gmx I get the following error: Fatal error: Residue '' not found in residue topology database I'm a beginner GROMACS user, but I want to know exactly,

Re: [gmx-users] Fw: energy minimization problem

On 11/4/13 3:29 AM, kiana moghaddam wrote: Dear Justin Further to your previous email, I want to calculate free energy for DNA-ligand interaction. According to your answer, for more sensitive calculations like free energy simulations and normal modes, emtol should be lower than 1. As I

Re: [gmx-users] gmxcheck

On 11/4/13 5:06 AM, Ankita Naithani wrote: Hi, I was wondering if anyone could help me with the gmxcheck function? In the manual it is written, -m flag is given a LaTeX file will be written consisting of a rough outline for a methods section for a paper. I tried it several times but there

Re: [gmx-users] gmxcheck

Hi Justin, Thank you for your reply. I did give the .tpr file but the job terminated after few frames only. Also, if that is not helpful, do you have any suggestions to recover the essential information which you would include as part of methods? Kind regards, Ankita On Mon, Nov 4, 2013 at

Re: [gmx-users] gmxcheck

On 11/4/13 7:14 AM, Ankita Naithani wrote: Hi Justin, Thank you for your reply. I did give the .tpr file but the job terminated after few frames only. Also, if that is not helpful, do you have any There are no frames in a .tpr file. I suspect you're simply issuing the command incorrectly,

Re: [gmx-users] gmxcheck

I do have the .mdp file. Main thing I was concerned about were details like number of water molecules added and number of counter ions added. Does gmxdump output that information? On Mon, Nov 4, 2013 at 12:19 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/4/13 7:14 AM, Ankita Naithani

Re: [gmx-users] gmxcheck

On 11/4/13 7:37 AM, Ankita Naithani wrote: I do have the .mdp file. Main thing I was concerned about were details like number of water molecules added and number of counter ions added. Does gmxdump output that information? Yes, buried in a long list of other things. Trivial details like

Re: [gmx-users] Re: Hardware for best gromacs performance?

just a small benchmark... each node - 2 x Xeon E5-2680v2 + 2 x NVIDIA K20X GPGPUs 42827 atoms - vsites - 4fs 1 node142 ns/day 2 nodes FDR14 218 ns/day 4 nodes FDR14 257 ns/day 8 nodes FDR14 326 ns/day 16 nodes FDR14 391 ns/day (global warming) best, timo -- gmx-users mailing list

Re: [gmx-users] gmxcheck

Thanks Justin very much for your help. (Extremely silly and unthoughtful of me to forget this) Kind regards, Ankita On Mon, Nov 4, 2013 at 12:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/4/13 7:37 AM, Ankita Naithani wrote: I do have the .mdp file. Main thing I was concerned about

Re: [gmx-users] Fw: energy minimization problem

Dear Justin It is obvious that emtol value can not be zero or negative. but you wrote in  your email  For more sensitive calculations like free energy simulations and normal modes, you will want to minimize much more thoroughly (for NM, emtol 1) and in double precision. what did you mean by

Re: [gmx-users] Fw: energy minimization problem

On 11/4/13 8:55 AM, kiana moghaddam wrote: Dear Justin It is obvious that emtol value can not be zero or negative. but you wrote in your email For more sensitive calculations like free energy simulations and normal modes, you will want to minimize much more thoroughly (for NM, emtol 1) and

Re: [gmx-users] Re: Hardware for best gromacs performance?

Brad, These numbers seems rather low for a standard simulation setup! Did you use a particularly long cut-off or short time-step? Cheers, -- Szilárd Páll On Fri, Nov 1, 2013 at 6:30 PM, Brad Van Oosten bv0...@brocku.ca wrote: Im not sure on the prices of these systems any more, they are

Re: [gmx-users] Hardware for best gromacs performance?

Hi David, Do you want to maximize throughput with multiple simulations or you want single simulations as fast as possible? In general, as few and fast CPU(s)/GPU(s) is best - especially with such small systems as yours which won't scale very well to more than 1-2 GPUs. As I previously mentioned

Re: [gmx-users] Gromacs-4.6 on two Titans GPUs

You can use the -march=native flag with gcc to optimize for the CPU your are building on or e.g. -march=corei7-avx-i for Intel Ivy Bridge CPUs. -- Szilárd Páll On Mon, Nov 4, 2013 at 12:37 PM, James Starlight jmsstarli...@gmail.com wrote: Szilárd, thanks for suggestion! What kind of CPU

Re: [gmx-users] Re: Installation Gromacs 4.5.7 on rocluster cluster with centos 6.0

On Mon, Nov 4, 2013 at 12:01 PM, bharat gupta bharat.85.m...@gmail.comwrote: Hi, I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works fine till .configure command, but I am getting error at the make command :- Error: [root@cluster gromacs-4.5.7]#

[gmx-users] Group protein not found in indexfile

Hello I am just trying to do a simple MD on a dimmer system (in which the dimmers are NOT identical). I can use pdb2gmx to create a topology file and four .itp files pores.chainA.itp, pores.chainX.itp; system.Protein.chainA.itp and system.Protein.chainX.itp. When I use grompp however, I

[gmx-users] Analysis tools and triclinic boxes

Dear all, I am using gromacs 4.6.3 with a triclinic box. Based on the manual and mail list, it is my understanding that the default box shape in gromacs in a triclinic box. Can I assume that all the analysis tools also work for a triclinic box. Cheers, Stephanie -- gmx-users mailing list

Re: [gmx-users] Group protein not found in indexfile

On 11/4/13 1:29 PM, Steve Seibold wrote: Hello I am just trying to do a simple MD on a dimmer system (in which the dimmers are NOT identical). I can use pdb2gmx to create a topology file and four .itp files pores.chainA.itp, pores.chainX.itp; system.Protein.chainA.itp and

Re: [gmx-users] Analysis tools and triclinic boxes

On 11/4/13 1:29 PM, Stephanie Teich-McGoldrick wrote: Dear all, I am using gromacs 4.6.3 with a triclinic box. Based on the manual and mail list, it is my understanding that the default box shape in gromacs in a triclinic box. Can I assume that all the analysis tools also work for a triclinic

Re: [gmx-users] TFE-water simulation

Thanks Joao Henriques for helping me with the steps. On Nov 4, 2013 3:18 PM, João Henriques joao.henriques.32...@gmail.com wrote: Hello Archana, I'm also toying with a TFE-water system, therefore I am also a newbie. This is what I am doing, I hope it helps: 1) Since I'm using G54A7 I

Re: [gmx-users] Gentle heating with implicit solvent

Dear Mark, Sorry for replying to an older thread. We are trying to perform implicit solvent simulations of protein G with CHARMM27 in gromacs. We are trying to trouble shoot why the protein unfolds after already 2 ns of dynamics. We use simulated annealing for the heating with 1 fs time step.

[gmx-users] Group protein not found in indexfile

Hi Justin Thanks for your response. Here are the files you asked for. They are all text files. I am still attempting to fix this, but am still getting the error I described no matter what I have done so far. Thanks again, Stevegrompp -f pr.mdp -n pr.ndx -c prbox.pdb -p system.top -o pr.tpr --

Re: [gmx-users] Group protein not found in indexfile

On 11/4/13 3:03 PM, Steve Seibold wrote: Hi Justin Thanks for your response. Here are the files you asked for. They are all text files. I am still attempting to fix this, but am still getting the error I described no matter what I have done so far. The list does not accept attachments,

Re: [gmx-users] Gentle heating with implicit solvent

On 11/4/13 2:25 PM, Gianluca Interlandi wrote: Dear Mark, Sorry for replying to an older thread. We are trying to perform implicit solvent simulations of protein G with CHARMM27 in gromacs. We are trying to trouble shoot why the protein unfolds after already 2 ns of dynamics. We use simulated

[gmx-users] .top file for a mixed solvent

Hi gmx users, I want to simulate ionomer is mixed solution of water and ethanol using gromos force field. I tired to follow the steps suggested on gromacs website, which are: 1- Determine the number of co-solvent molecules necessary, given the box dimensions of your system. 2- Generate a

RE: [gmx-users] Different Residues...

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304

RE: [gmx-users] Calculation of water density around certain protein residues

You have a number of molecules, you know what those molecules are, you can calculate their mass, you know the volume, therefore you can calculate a density. For the average for entire simulation, simply pass the water.xvg file to g_analyze There is all the information you require right there

Re: [gmx-users] .top file for a mixed solvent

On 11/4/13 5:25 PM, Ehsan Sadeghi wrote: Hi gmx users, I want to simulate ionomer is mixed solution of water and ethanol using gromos force field. I tired to follow the steps suggested on gromacs website, which are: 1- Determine the number of co-solvent molecules necessary, given the box

Re: [gmx-users] Gentle heating with implicit solvent

Hi Justin, We are using infinite cutoffs (all vs all). Here is the mdp file for the heating (please note that -DPOSRES is commented out) and the time step is 1 fs: ; VARIOUS PREPROCESSING OPTIONS = title= cpp = /lib/cpp include =

[gmx-users] Re: Using gromacs on Rocks cluster

Hi, I have installed Gromcas 4.5.6 on Rocks cluster 6.0 andmy systme is having 32 processors (cpu). But while running the nvt equilibration step, it uses only 1 cpu and the others remain idle. I have complied the Gromacs using enable-mpi option. How can make the mdrun use all the 32 processors ??

[gmx-users] Fwd: Using gromacs on Rocks cluster

Hi, I have installed Gromcas 4.5.6 on Rocks cluster 6.0 andmy systme is having 32 processors (cpu). But while running the nvt equilibration step, it uses only 1 cpu and the others remain idle. I have complied the Gromacs using enable-mpi option. How can make the mdrun use all the 32 processors ??

[gmx-users] choosing force field

Dear all I would like to carry out unfolding simulations of my dimeric protein and would like to know which is the better force field to work with out of gromos 96 43 or 53? Also, is gromos 96 43a1 force field redundant? When I searched the previous archive, I could see similar question was

[gmx-users] Diffusion/PBC

Dear All, I have an problem related to jumping trajectory. In my MD run, there is a receptor molecule which is binding with an halogen anion in water solvent. In the original trajectory, the binding between them looks fine but jumping present. To remove the jumping of the system from