[gmx-users] About MD
xnzgxj at gmail.com
Mon Sep 26 09:31:39 CEST 2011
Hi, many thanks for your answer.
>> Any dynamical simulation has a lowest-energy structure... whether this
means anything is another question.
I am just wondering whether the structures you find with MD determined
mainly by thermodynamics (i.e. the lowest energy structures) or by kinetics
(i.e. the structures
with the lowest activation barriers)?
I wonder to know how can I set the parameters and in which condition I
obtain the structure by thermodynamics, and in which condition (with which
parameter setting) I can obtain the structure by kinetics.
>> MD samples the free-energy surface. Its shape and the temperature
determine what structures might be found, and in what proportions.
Do you mean that I can obtain the structure by thermodynamics in longer and
higher temperature ; obtain the structure by kinetics in shorter and lower
2011/9/26 Mark Abraham <Mark.Abraham at anu.edu.au>
> 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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