[gmx-users] About MD

[Mark Abraham]

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.

Mark