[gmx-users] About MD

[xiaojing gong]

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
temperature?



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.
>
> Mark
> --
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