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There is a way to extract the PMF from sMD simulations using the
weighted histogram analysis method (WHAM) in gromacs- Justin
Lemkul's tutorial does a nice job of explaining it:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html</a><br>
<br>
- Laura<br>
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<br>
<br>
On 10/31/2011 11:05 AM, Sanku M wrote:
<blockquote
cite="mid:1320073543.62955.YahooMailNeo@web114411.mail.gq1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff; font-family:times
new roman, new york, times, serif;font-size:12pt">
<div style="font-family: 'times new roman', 'new york', times,
serif; font-size: 12pt; ">Hi,</div>
<div><font class="Apple-style-span" face="'times new roman',
'new york', times, serif" size="3"> I have done some
steered MD simulation and I want to construct the potential
of mean force from these pull-profile using Jarzinsky's </font><font
class="Apple-style-span" face="'times new roman', 'new
york', times, serif">inequality</font><font
class="Apple-style-span" face="'times new roman', 'new
york', times, serif" size="3">. I wanted to see whether, in
updated version of gromacs, there is any implementation of
extracting PMF from SMD simulations. </font></div>
<div><font class="Apple-style-span" face="'times new roman',
'new york', times, serif" size="3">If not, can anyone
suggest some guidelines how to do it.</font></div>
<div><font class="Apple-style-span" face="'times new roman',
'new york', times, serif" size="3">Sanku</font></div>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Laura Kingsley
Graduate Student
Medicinal Chemistry and Molecular Pharmacology
Purdue University
Office: RHPH 504A
575 Stadium Mall Dr.
West Lafayette, IN 47907
Office Phone: (765) 496-6643</pre>
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