[gmx-users] About MD

[xiaojing gong]

Hi, many thanks.
I am doing some simulation correlated with the growth, in experiments, there
are two kinds of growth, one is driven by kinetics and other is  by
thermodynamics. So I just wonder to know by using MD simulations, the
results I obtained is driven by  kinetics or thermodynamics.

Silly question.

XJ

2011/9/26 Mark Abraham <Mark.Abraham at anu.edu.au>

>  On 26/09/2011 5:31 PM, xiaojing gong wrote:
>
> 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?
>
>
> You are drawing some artificial distinction whose purpose I do not
> understand.  A short simulation on a FES at a temperature low enough that
> the barriers are larger than the readily available KE will be kinetically
> trapped. I'd guess that most MD simulations that have ever been run have
> suffered from this defect. The shape of the FES will generally vary with
> temperature also.
>
> Mark
>
>
>
>
>
> 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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>
>
>
>
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