[gmx-users] Protein fragments during production simulation

[SAPNA BORAH]

Dear Justin,

Thanks for the clarification. :)

Regards,
Sapna

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
>> 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
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
Sapna Mayuri Borah
Research student
Tezpur University,
India