<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Hi Laura,</span></div><div><span> I do not think Justin Lemkul's tutorial is suggesting extracting PMF using SMD simulation. What is does that it uses SMD to generate the initial configurations for different windows and then perform umbrella sampling separately on each windows to subsequently extract the PMF using WHAM based on the data set on umbrella sampling.</span></div><div><br></div><div>Sanku</div><div><br></div><div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "><div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "><font size="2" face="Arial"><hr size="1"><b><span style="font-weight:bold;">From:</span></b> Laura Kingsley <lkingsle@purdue.edu><br><b><span style="font-weight: bold;">To:</span></b> gmx-users@gromacs.org<br><b><span
style="font-weight: bold;">Sent:</span></b> Monday, October 31, 2011 11:09 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Jarzinsky's inequality from SMD simulation<br></font><br>
<meta http-equiv="x-dns-prefetch-control" content="off"><div id="yiv517061180">
<div>
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>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html<br>
<br>
- Laura<br>
<br>
<br>
<br>
On 10/31/2011 11:05 AM, Sanku M wrote:
<blockquote type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; ">
<div style="font-size: 12pt; font-family: times, serif; ">Hi,</div>
<div><font class="yiv517061180Apple-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="yiv517061180Apple-style-span" face="'times new roman', 'new
york', times, serif">inequality</font><font class="yiv517061180Apple-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="yiv517061180Apple-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="yiv517061180Apple-style-span" face="'times new roman',
'new york', times, serif" size="3">Sanku</font></div>
</div>
</blockquote>
<br>
<pre class="yiv517061180moz-signature">--
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>
</div>
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