AMBER Archive (2009)

Subject: [AMBER] Re: reference re. size of dt

From: case (case_at_biomaps.rutgers.edu)
Date: Mon Jul 13 2009 - 11:56:46 CDT

On Mon, Jul 13, 2009, Paul Brandt wrote:
> Dear Dr. Case,

Please send amber-related questions to the mail reflector, amber_at_ambermd.org,
and not to me personally. That way, many people can see your question and try
to help, and the answers can help others with similar questions. See
http://lists.ambermd.org/mailman/listinfo/amber for information on how to
subscribe.
>
> I would like to understand how the upper-limit for the size of time steps is
> determined for the integration of the equations of motion in a simulation.
> I asked on the amber mail list if anyone knew of a good reference, but I got
> no reply.

I imagine people didn't answer because it's not clear what you have already
read. Be sure to check Allen and Tildesley; Tamar Schlick's book has a lot on
this subject as well. A quick Google search on "time step molecular dynamics"
leads here:

   http://en.wikipedia.org/wiki/Energy_drift

Maybe that will help.....dac

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