[gmx-users] Protein fragments during production simulation

[Tsjerk Wassenaar]

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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