[gmx-users] Protein fragments during production simulation

Justin Lemkul jalemkul at vt.edu
Thu Apr 30 19:32:05 CEST 2015

On 4/30/15 10:12 AM, SAPNA BORAH wrote:
> Dear all,
> I have some doubts regarding pbc being new to gromacs. Since my protein was
> breaking into fragments, I introduced pbc options and found the trajectory
> whole and centred in the water box, but this was done after the simulation
> and just for taking the snapshots with the command prompt:
> trjconv -s run.tpr -f run.xtc -pbc mol -center -skip 500 -sep -o step.pdb
> Is this the correct way to do it or do I have to incorporate pbc in the
> .mdp files and re-run the simulation.

You do not need to alter the .mdp file.

> Also, before that I also checked if equilibration was an issue. So I
> extended equilibration of the system to 5ns and 10ns. The results(without
> using pbc) after a 10ns production run for both 5ns and 10ns equilibration
> run shows that the protein is whole, however it had started breaking in
> fixed intervals at fixed amino acid residues and then becomes whole for
> around 2 ns and again fragments. The number of fragments has reduced
> comparatively to the 1ns equilibration run.
> Is this also a pbc related issue, and can someone please put some light on
> what exactly is the problem going on?

These are just visualization quirks.  This is exactly what PBC does and is 
entirely normal.  The physics don't depend on our ability to conveniently look 
at something :)



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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