[gmx-users] Protein fragments during production simulation

[SAPNA BORAH]

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