[gmx-users] request

I am beginner with gromacs. I would like to simulate the behavior of glassy materials starting with simple Lennard Jones liquid. please advise me as to how to begin. a relevent flowchart or tutorial would be of immerse help thank you very much indeed. -- gmx-users mailing listgmx-users@gromacs

Re: [gmx-users] Position restrained..

On 21/11/2010 4:01 AM, pawan raghav wrote: Dear All, Hope this mail will find you in good health. I am facing a problem regarding Position restrained dynamics (PR). I have done Molecular dynamic simulation (for cytosolic protein) but has not performed PR. So i m little confused if this effects

[gmx-users] Position restrained..

Dear All, Hope this mail will find you in good health. I am facing a problem regarding Position restrained dynamics (PR). I have done Molecular dynamic simulation (for cytosolic protein) but has not performed PR. So i m little confused if this effects the results and if yes to what extent it effe

[gmx-users] xtc corrupted during REMD

Hi there, I am encountering a weird problem with a REMD simulation using 4.5.3. The total simulation is 50ns with 5 replica, and I do in two runs: 25ns and then continuing to 50ns (walltime queue). The first run is okay, the continue run (the last 25ns) randomly make some xtc files corrupted (fr

Re: [gmx-users] Pairwise forces

On Fri, Nov 19, 2010 at 12:15, Reiner Ribarics wrote: > Our group has already done some rather long simulations and according to the > script files forces are written every 1 steps and can be accessed via > trjconv with -cf option that assigns each atom a temperature factor. I was > wondering

[gmx-users] g_hbond -ac -life

Dear gromacs users I used g_hbond -f .trr -s .tpr -n .ndx -ac -life. Can anyone clarify last 2 columns in hblife.xvg and last 4 columns hbac.xvg files by details. Also, I want to know what is difference between p(t) in hblife.xvg and c(t) in hbac.xvg file? which of them is more suitable for HB life

Re: [gmx-users] disparity in RMSD calculation

On Sat, 20 Nov 2010 19:05:35 +1100, Mark Abraham wrote > On 20/11/2010 4:54 PM, Sunita Patel wrote: > > Dear Users, > > > > I calculated RMSD for a trajectory with same reference structure using > > GROMACS > > and VMD. I observed completely difference plots for the same data. Please > > see > >

RE: [gmx-users] disparity in RMSD calculation

With topol.tpr file, am getting identical plot as that of VMD. Thanks, Sunita On Sat, 20 Nov 2010 08:39:17 +, X Rules wrote > I have had a similar experience, I have not investigated it thoroughly at the > moment, but I get different (identical with specific jumps possibly due to > pbc) plot

RE: [gmx-users] disparity in RMSD calculation

I have had a similar experience, I have not investigated it thoroughly at the moment, but I get different (identical with specific jumps possibly due to pbc) plots if I take starting structure as my input pdb file or if my starting structure is first structure of trajectory. I think the plots

Re: [gmx-users] add a group to an amino acid

Thank you very much, Mark! The problem was for the type CG2 in .rtp. I corrected it and the errors disappear.[?] (I should study more for that non-zero charge, i think.) <<332.gif>>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] disparity in RMSD calculation

On 20/11/2010 4:54 PM, Sunita Patel wrote: Dear Users, I calculated RMSD for a trajectory with same reference structure using GROMACS and VMD. I observed completely difference plots for the same data. Please see the attached file. What could be the cause for this disparity? We can't be defin