[gmx-users] About MD

[Mark Abraham]

On 26/09/2011 6:25 PM, xiaojing gong wrote:
> 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.

To address this question, I think you need to seek a better description 
than "driven by thermodynamics". All processes are driven by thermodynamics.

> So I just wonder to know by using MD simulations, the results I 
> obtained is driven by  kinetics or thermodynamics.

The two growth modes must differ somehow in the conditions that trigger 
them. For a valid model, which mode you might see will depend what 
conditions you choose.

Mark

>
> Silly question.
>
> XJ
>
> 2011/9/26 Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto: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
>>     <mailto: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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