[gmx-users] total simulation time for proteins in general

Priya Chandran priyachandran at gmail.com
Wed Apr 11 07:26:40 CEST 2007

I am a beginner in GROMACS and I am using GROMACS to analyse the solution
structure of protein in water after initial homology/abinitio modelling. I
have already run a search on the gmx_users list for my queries. There are a
few basic questions i would like to ask.

1. In the  md integrator, what is the total simulation time used in
simulation of peptides in general? I'm currently using 200ps, consisting of
nsteps=100000, and dt=0.002 and the rmsd graph has not reached a plateau
region still.

2. Is minimisation in GROMACS only used as a precursor to the md-simulation
to remove bad contacts, or can we also use it effectively to minimize a raw
modelled ab-initio structure.?

any help would be greatly appreciated.

Thanking you,

yours sincerely,
Priya Chandran

Dept. of Physics
Indian Institute of Science
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