[gmx-users] Protein fragments during production simulation
sapnauser365 at gmail.com
Fri May 1 20:11:04 CEST 2015
Thanks for the clarification. :)
On 4/30/15, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> breaking into fragments, I introduced pbc options and found the
>> whole and centred in the water box, but this was done after the
>> 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
>> 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
>> 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
> 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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Sapna Mayuri Borah
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