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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