Hi, many thanks. <br>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.<br>
<br>Silly question.<br><br>XJ<br><br><div class="gmail_quote">2011/9/26 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 26/09/2011 5:31 PM, xiaojing gong wrote:
<blockquote type="cite">Hi, many thanks for your answer.<br>
<br>
>> Any dynamical simulation has a lowest-energy structure...
whether this means anything is another question.<br>
<br>
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 <br>
with the lowest activation barriers)?<br>
<br>
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. <br>
<br>
>> MD samples the free-energy surface. Its shape and the
temperature determine what structures might be found, and in what
proportions.<br>
<br>
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?<br>
</blockquote>
<br></div>
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.<br><font color="#888888">
<br>
Mark</font><div class="im"><br>
<br>
<blockquote type="cite"><br>
<br>
<br>
<div class="gmail_quote">2011/9/26 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>On 26/09/2011 6:41 AM, xiaojing gong wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear all£¬<br>
A question about, in MD, in which situation you can obtain
a structure with lowest energy.<br>
</blockquote>
<br>
</div>
Any dynamical simulation has a lowest-energy structure...
whether this means anything is another question.
<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Can MD simulate the kinetics process, and obtain a
stuctrue with the lowest activation barriers?<br>
</blockquote>
<br>
</div>
Mapping free-energy surfaces where bonds are not made or
broken can be done with conventional MD.
<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Typically, are the structures we find with MD determined
mainly by thermodynamics or by kinetics ?<br>
</blockquote>
<br>
</div>
MD samples the free-energy surface. Its shape and the
temperature determine what structures might be found, and in
what proportions.<br>
<br>
Mark<br>
<font color="#888888">
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