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.abra...@anu.edu.au <mailto:mark.abra...@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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