[gmx-users] total simulation time for proteins in general
Mark.Abraham at anu.edu.au
Wed Apr 11 07:39:09 CEST 2007
Priya Chandran wrote:
> 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.
This is totally dependent on the system in question and what you expect
the time-scale of relevant motions to be. I'd expect 200ps is at least
an order of magnitude too short to have any basis for confidence that a
solution structure is stable for a given forcefield.
> 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.?
Well, yes, you can use it for this - they're both the same objective,
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