[gmx-users] Time step in md

Jussi Lehtola jussi.lehtola at helsinki.fi
Fri Sep 19 21:22:46 CEST 2008

On Fri, 2008-09-19 at 20:35 +0400, DimitryASuplatov wrote:
> Hello,
> could you explain my the secret of choosing to time step for md
> integrator? I want to perform a 10-20 ns simulation in water in order
> to, for ex., calculate some interactions or to see if the structure
> would relax to a stable state. 
> If I use vsites, heavyh and LINCS I can run with 6 fs step. This would
> be quite quick. 
> I just wonder if this is `by book`. 
> I appreciate your help.

Turn off any thermostats you have on (perform an NVE run) and then try
out short runs (say, 5000 steps) with different time steps. Plot out the
total energy graphs for the different runs.

If your time step is too big you'll end up with total energy either
increasing or decreasing. With a very big time step you might end up
with an exploding system..

If you use constraints you are able to use larger time steps.
With hydrogen bond length constraints the time step is about 2 fs, if
the molecules are flexible the time step needs to be a lot smaller,
since hydrogen atoms oscillate very fast because of their small mass.
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.lehtola at helsinki.fi, p. 191 50623
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.lehtola at helsinki.fi

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