<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 26/09/2011 6:25 PM, xiaojing gong wrote:
<blockquote
cite="mid:CAOm9RSX9i=UyaF2wnNLe5K0rGEmYfpX2w7nqf0gSASvgeCb1AQ@mail.gmail.com"
type="cite">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.</blockquote>
<br>
To address this question, I think you need to seek a better
description than "driven by thermodynamics". All processes are
driven by thermodynamics.<br>
<br>
<blockquote
cite="mid:CAOm9RSX9i=UyaF2wnNLe5K0rGEmYfpX2w7nqf0gSASvgeCb1AQ@mail.gmail.com"
type="cite"> So I just wonder to know by using MD simulations, the
results I obtained is driven by kinetics or thermodynamics.<br>
</blockquote>
<br>
The two growth modes must differ somehow in the conditions that
trigger them. For a valid model, which mode you might see will
depend what conditions you choose.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAOm9RSX9i=UyaF2wnNLe5K0rGEmYfpX2w7nqf0gSASvgeCb1AQ@mail.gmail.com"
type="cite">
<br>
Silly question.<br>
<br>
XJ<br>
<br>
<div class="gmail_quote">2011/9/26 Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true" 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 moz-do-not-send="true"
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"> -- <br>
gmx-users mailing list <a
moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a
moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the
list. Use the www interface or send it to <a
moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></blockquote>
</div>
<br>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div>
</div>
<br>
--<br>
gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</blockquote>
</div>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>