[gmx-users] About MD

[Mark Abraham]

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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