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><br><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 class="im">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 class="im"><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 class="im"><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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