[gmx-users] Protein fragments during production simulation

SAPNA BORAH sapnauser365 at gmail.com
Tue Apr 28 06:25:55 CEST 2015

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:

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.

Sapna Mayuri Borah
Research Student
Tezpur University

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