Re: Why minimization before Molecular Dynamics?

From: Luca Muccioli (
Date: Thu Mar 15 2007 - 06:50:43 CDT

On Thu, 15 Mar 2007, Pedro Borkowski wrote:

> Hey,
> I was wondering why is it necessary to minimize the system before
> running molecular dynamics.
> I was wondering what would happen if the system was not minimized
> before running molecular dynamics.
> Many thanks

dear Pedro,
 depending on the tools that you use for building the starting
configuration, it may happen than some molecules/atoms result partially
superimposed. This leads to strongly repulsive forces and enormous
velocities, that determine the "explosion" of the sample or the crash of
your run; both things can be easily circunvented with a small preliminary
minimization. An alternative can be using a very tiny timestep at the
beginning, but doesn't always work.




Luca Muccioli, Ph. D.
Dipartimento di Chimica Fisica e Inorganica
Universita` di Bologna
Via Risorgimento 4
40136 Bologna (Italia)

Phone: +39-051-6446992
Fax: +39-051-2093690

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