[gmx-users] Warnings while grompp_d

Hi there, while running gromacs in parallel with double precision, during grompp_d I am getting following warning in output file along with other status.. ... ... ... WARNING 1 [file 1XU9_A.top, line unknown]: The largest charge group contains 12 atoms. Since atoms only see each other when th

Re: [gmx-users] Re: trjconv error

You seem not to get it... I specifically chew out for you that you need to give a listing using the command ls -l. That will also show what the size of the file is. This is completely pointless this way! Also, you only now state the command you gave. Now, rereading the first mail, it also said ..t

Re: [gmx-users] Warnings while grompp_d

vivek sharma wrote: Hi there, while running gromacs in parallel with double precision, during grompp_d I am getting following warning in output file along with other status.. ... ... ... WARNING 1 [file 1XU9_A.top, line unknown]: The largest charge group contains 12 atoms. Since atoms on

Re: [gmx-users] How to use g_energy after parellal mdrun

vivek sharma wrote: Hi Jochen, Thanks for your response. That was some syntax error, now I am getting only single .edr file. Is there any restriction in mdp file parameters while running it in parallel mode ? And, is it necessary to run energy minimization and position restraining before runn

Re: [gmx-users] Corrupt TRR file -- skipping a bad frame?

I'm sure I have, in the past, found a way to use trjcat/trjconv to overwrite a bad frame with a good one.  From memory, I had to convert the area around the bad frame to pdb/gro (for some reason that worked where normal tools didn't), open up the files, rewrite several bad frames (just copied an

[gmx-users] problems creating mixed solvent systems

Good day to you! I'm new to MD and this is my first time bugging you with issues I don't seem to be able to solve on my own (using the archive and the manual), so I hope you bare with me and can possibly offer me a sanity check or some alternative approaches to my problem. As I have already i

[gmx-users] M*tif installation

Using google returns no good results, would anybody help me about this? Configure grace did not succeed.. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gro

Re: [gmx-users] M*tif installation

Ross KK Leung wrote: Using google returns no good results, would anybody help me about this? Configure grace did not succeed…. Having no idea what you're doing, I doubt anyone here can provide any useful advice. Furthermore, this list is for Gromacs-related questions, not Grace. Try th

Re: [gmx-users] problems creating mixed solvent systems

Ted Fischer wrote: Good day to you! I'm new to MD and this is my first time bugging you with issues I don't seem to be able to solve on my own (using the archive and the manual), so I hope you bare with me and can possibly offer me a sanity check or some alternative approaches to my proble

RE: [gmx-users] M*tif installation

Then how would you analyze the MD results? Because Gromacs output is an xvg file and Google returns very few results about it... -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Justin A. Lemkul Sent: Thursday, August 28, 2008 5:54 PM To: Discussion list fo

Re: [gmx-users] M*tif installation

Ross KK Leung wrote: Then how would you analyze the MD results? Because Gromacs output is an xvg file and Google returns very few results about it... I'm not saying you shouldn't use Grace. All you've told us is that you could not configure Grace. Without any details (system type, compile

Re: [gmx-users] M*tif installation

Hi, On Thursday, 28. August 2008, Ross KK Leung wrote: > Then how would you analyze the MD results? Because Gromacs output is an xvg > file and Google returns very few results about it... it is a plain text file. Per default xmgrace files are written by gromacs http://plasma-gate.weizmann.ac.

Re: [gmx-users] M*tif installation

Hey, And on top of that, you don't need to get any of these grace related tags which make it 'xvg'. You can use the flag -noxvg with about any tool and get nothing but the raw data. (One could also use grep -v "[EMAIL PROTECTED]" something.xvg to remove the grace directives). And that makes a fou

[gmx-users] Re: M*tif installation

>> Using google returns no good results, would anybody help me about this? >> Configure grace did not succeed…. You are absolutely right. Install MOTIF. What's the problem? -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMA

[gmx-users] Disappear my solution

Dear I have a box with 2 different kind of solution and one protein. Actually, I minized my box in each step which i add matter to box. After minimization of my system I run it for 10 ns. unfortunately after 1.3 ns one of my solution dissapear. eg, I have hexan organic solvent, water and protein,

[gmx-users] g_hbond + invalid command line argument -g

Hi all, I am new to gromacs, I am interested in calculate Hydrogen bonds of my protein. So I have issued the *g_hbond command like this g_hbond -f .xtc -s .tpr -n .ndx(Index file contain all residues mainchain+H atoms) -num .xvg -g .log its showed Program g_hbond, VERSION 3.3.1 Source co

Re: [gmx-users] g_hbond + invalid command line argument -g

minnale wrote: Hi all, I am new to gromacs, I am interested in calculate Hydrogen bonds of my protein. So I have issued the *g_hbond command like this g_hbond -f .xtc -s .tpr -n .ndx(Index file contain all residues mainchain+H atoms) -num .xvg -g .log its showed Program g_hbond, VERSION

Re: [gmx-users] Disappear my solution

Morteza Khabiri wrote: Dear I have a box with 2 different kind of solution and one protein. Actually, I minized my box in each step which i add matter to box. After minimization of my system I run it for 10 ns. unfortunately after 1.3 ns one of my solution dissapear. eg, I have hexan organic s

Re: Re: [gmx-users] g_hbond + invalid command line argument -g

Thanks Justin for your quick reply the g_hbond command ran succesfully and gave me .xvg file and it contain 3 columns that is like @title "Hydrogen Bonds" @xaxis label "Time" @yaxis label "Number" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend locty

Re: Re: [gmx-users] g_hbond + invalid command line argument -g

Thanks Justin for your quick reply the g_hbond command ran succesfully and gave me .xvg file and it contain 3 columns that is like @title "Hydrogen Bonds" @xaxis label "Time" @yaxis label "Number" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend locty

[gmx-users] compare 3.3.3 vs 3.99.4 (bit long)

Dear all, I am using the Louhi cluster on the Finnish IT center (http://www.csc.fi/english) and I had the chance to test the latest beta version of gromacs (3.99.4). First of all I have to say that it is very fast and very scalable. Now, reliability. I have run a 2ns simulation of a protein in wate

Re: [gmx-users] g_hbond + invalid command line argument -g

minnale wrote: Thanks Justin for your quick reply the g_hbond command ran succesfully and gave me .xvg file and it contain 3 columns that is like @title "Hydrogen Bonds" @xaxis label "Time" @yaxis label "Number" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box

Re: [gmx-users] M*tif installation

Ross KK Leung wrote: > Then how would you analyze the MD results? Because Gromacs output is an xvg > file and Google returns very few results about it... > In my Ubuntu box the dependency is solved by the lesstif2 library. You can look for lesstif library for your own system (you should provide

[gmx-users] Disappear my solution

Dear Thanks for your prompt reply. In gro file everything is ok. during the run I just load my XTC file by vmd visual software and i saw that after 1.3 ns suddenly hexan disappear and my system just have protein and water. the most strange things is that the place of hexan is empty and is not full

Re: [gmx-users] Disappear my solution

Morteza Khabiri wrote: Dear Thanks for your prompt reply. In gro file everything is ok. during the run I just load my XTC file by vmd visual software and i saw that after 1.3 ns suddenly hexan disappear Did you restart your run after that short time? Did you change the xtc-grps option in y

[gmx-users] LJ question

Dear Users: I am planing to do some simulations of a protein in acetonitrile using the model of P.J. Gee (Mol. Phys. (2006) 104, 477-483). The use of this model will introduce new atom types and new LJ parameters for those atoms. When I define those atoms in the acetonitrile topology I need to d

[gmx-users] Disappear my solution

Dear Justin Thanks for your helps. --Did you restart your run after that short time? Did you change the xtc-grps option in your .mdp file? no. I did not change any option and also not restart my run. --That would be pretty strange. If they were there, then disappeared, maybe they were not

Re: [gmx-users] LJ question

Anthony Cruz wrote: Dear Users: I am planing to do some simulations of a protein in acetonitrile using the model of P.J. Gee (Mol. Phys. (2006) 104, 477-483). The use of this model will introduce new atom types and new LJ parameters for those atoms. When I define those atoms in the acetonitril

Re: [gmx-users] Disappear my solution

Morteza Khabiri wrote: Yes. after disappear, the vmd console show an error. it is: Error reading timestep, file does not match format. What does gmxcheck tell you about the file? Maybe there was a hardware blip or something that messed up a frame in the .xtc file. As I said everything

[gmx-users] Re: gmx-users Digest, Vol 52, Issue 109

Hi Justin, well, actually the problem is not only with grompp, since my non integer charges come all the way since pdb2gmx I used as I told: pdb2gmx -f 1vkxdna.pdb -o 1vkxdna.gro -p 1vkxdna.top editconf -f 1vkxdna.gro -o 1vkxdna_caixa.gro -c -d 0.9 -princ genbox -cs -cp 1vkxdna_caixa.gro -o 1vkxdna

Re: [gmx-users] LJ question

Thank you for your rapidly responce David. If I use thr Gromos96 (ff43a1) it will do it? How I check if the force field allows mixing? Cheers, Anthony On Thursday 28 August 2008 01:34:30 pm David van der Spoel wrote: > Anthony Cruz wrote: > > Dear Users: > > I am planing to do some simulations o

[gmx-users] (no subject)

Greetings! I am trying to perform free energy calculations on my protein system. I am using Gromacs 3.3.3 double precision for Linux. The grompp runs fine and the .tpr file is created, but as soon as I submit the batch job, it dies and I receive the following error message Back Off! I just back

[gmx-users] mdrun failing with error message "reading tpx file (em.tpr) version 40 with version 31 program"

Greetings! I am trying to perform free energy calculations on my protein system. I am using Gromacs 3.3.3 double precision for Linux. The grompp runs fine and the .tpr file is created, but as soon as I submit the batch job, it dies and I receive the following error message Back Off! I just bac

Re: [gmx-users] LJ question

Anthony Cruz wrote: Thank you for your rapidly responce David. If I use thr Gromos96 (ff43a1) it will do it? How I check if the force field allows mixing? GROMOS does not use mixing rules in the same way as other force fields. This means it is more cumbersome, though not impossible. I'm not su

Re: [gmx-users] Re: gmx-users Digest, Vol 52, Issue 109

Ragnarok sdf wrote: Hi Justin, well, actually the problem is not only with grompp, since my non integer charges come all the way since pdb2gmx I used as I told: pdb2gmx -f 1vkxdna.pdb -o 1vkxdna.gro -p 1vkxdna.top editconf -f 1vkxdna.gro -o 1vkxdna_caixa.gro -c -d 0.9 -princ genbox -cs -cp 1vkx

[gmx-users] Disappear my solution

Dear Justin Thanks for your prompt reply and guide. As you said I checked my files with gmxcheck. My tpr file is ok. It includes water, hexan and protein. but my edr, xtc and trr files have problem. Their faults are as follow: 1- for xtc: Reading frame 110 time 550.000 Fatal error: Magic

Re: [gmx-users] Disappear my solution

Quoting Morteza Khabiri <[EMAIL PROTECTED]>: > Dear Justin > > Thanks for your prompt reply and guide. > > As you said I checked my files with gmxcheck. > > My tpr file is ok. It includes water, hexan and protein. but my edr, xtc > and trr files have problem. > Their faults are as follow: > > 1- f

[gmx-users] g_msd

Dear users, I am trying to calculate the diffusion coefficient for my protein using g_msd. I issued the following command: g_msd -f .xtc -s .pdb -o .xvg It gave me the diffusion coefficient as 0.068 (+/- 0.0279) * 10^-5 cm^2 s^ -1 (for my whole system). The shape of the plot is not linear rath

Re: Re: [gmx-users] g_hbond + invalid command line argument -g

Thanks Justin for your reply I am interested to get file which contain how many hydrogen bonds are there in my protein and the bonds present between which atoms? Is there anyway to get this file can you please tell me, Thanks in advance for your kind suggestion On Thu, 28 Aug 2008 Justin A

[gmx-users] a question about the content in atm-pair.out file

Hello all, Sorry to bother you, I have a question about the content in the file atm-pair.out file which is generated by the command g_mindist. Here is several lines of the file: " 0.00e+00 114 72 1.00e+01 114 72 2.00e+01 85 66 3.00e+01 85 65 4.00e+01 82 66 5.00e+01 1

[gmx-users] about connections

hello guys,   is there any idea how to extract no. of connections from trejectory? Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut   Check out the all-new face of

Re: [gmx-users] g_hbond + invalid command line argument -g

minnale wrote: Thanks Justin for your reply I am interested to get file which contain how many hydrogen bonds are there in my protein and the bonds present between which atoms? Is there anyway to get this file can you please tell me, g_hbond -h Thanks in advance for your kind suggestion

Re: [gmx-users] (no subject)

Hi Anjelika, The version of mdrun_mpi you're using is an older version of Gromacs (than used for setting up the simulation), not capable of reading the newer .tpr files. Be sure to use 3.3.3 also for the production run. Cheers, Tsjerk On Thu, Aug 28, 2008 at 7:47 PM, Anjelika Gasilina <[EMAIL P

Re: [gmx-users] problems creating mixed solvent systems

> What might be worth trying is starting with genconf. Use genconf -nbox (and > -dist, if necessary), starting from one MeOH molecule to generate a grid of > 400. > Then use genbox with -maxsol (and perhaps playing a bit with box > dimensions). > > -Justin Thanks for your perspective, I re