[gmx-users] Protein fragments during production simulation

[SAPNA BORAH]

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.


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?

Regards,
Sapna

On Wed, Apr 29, 2015 at 10:46 AM, SAPNA BORAH <sapnauser365 at gmail.com>
wrote:

> Hi Tsjerk,
>
> Thank your for your help. I could get over the issue. :)
>
> Regards,
> Sapna.
>
> On Tue, Apr 28, 2015 at 11:44 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
>> Hi Sapna,
>>
>> Check
>>
>> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>>
>> Cheers,
>>
>> Tsjerk
>> On Apr 28, 2015 6:26 AM, "SAPNA BORAH" <sapnauser365 at gmail.com> wrote:
>>
>> > Dear all,
>> >
>> > I am trying to simulate a globular protein predicted by Ab-initio method
>> > using web servers, Robetta and Itasser. I am currently using Gromacs
>> 4.6.5.
>> > A problem has occured during the production md run, when my protein
>> starts
>> > to break into fragments while it remains inside the water box.
>> >
>> > Energy minimisation is achieved in 15000 steps using steep gradient.
>> > Equilibration is run for 1ns.
>> > Production md is run for 100ns.
>> >
>> > My complete mdp file for production run in as follows:
>> >
>> > ------run.mdp------
>> > integrator = md
>> > nsteps = 50000000
>> > dt = 0.002
>> > nstlist = 10
>> > rlist = 1.0
>> > coulombtype = pme
>> > rcoulomb = 1.0
>> > cutoff-scheme = verlet
>> > vdw-type = cut-off
>> > rvdw = 1.0
>> > tcoupl = v-rescale
>> > tc-grps = protein non-protein
>> > tau-t = 0.1 0.1
>> > ref-t = 298 298
>> > nstxtcout = 1000
>> > nstenergy = 1000
>> > constraints = all-bonds
>> > ------------------
>> >
>> > Can you please help me with the issue?
>> >
>> > Thanking You.
>> >
>> > Regards,
>> > Sapna Mayuri Borah
>> > Research Student
>> > Tezpur University
>> > India
>> > --
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>
>
>
> --
> Sapna Mayuri Borah
> Research student
> Tezpur University,
> India
>



-- 
Sapna Mayuri Borah
Research student
Tezpur University,
India