[gmx-users] About MD
Mark.Abraham at anu.edu.au
Mon Sep 26 09:03:36 CEST 2011
On 26/09/2011 6:41 AM, xiaojing gong wrote:
> Dear all，
> A question about, in MD, in which situation you can obtain a structure
> with lowest energy.
Any dynamical simulation has a lowest-energy structure... whether this
means anything is another question.
> Can MD simulate the kinetics process, and obtain a stuctrue with the
> lowest activation barriers?
Mapping free-energy surfaces where bonds are not made or broken can be
done with conventional MD.
> Typically, are the structures we find with MD determined mainly by
> thermodynamics or by kinetics ?
MD samples the free-energy surface. Its shape and the temperature
determine what structures might be found, and in what proportions.
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