Hi Justin,<div><br></div><div>Thanks a lot for the reply.</div><div>Yes I have had a look at section 4.4.2. But section 5.3 tells that this WHAM can be used with the REMD data set as well. So my question is that how to present this REMD data of multiple trajectories as input to WHAM? Do I need to work around with the WHAM code or there is some other way?</div>
<div>Any suggestion is welcome. Thanks again.</div><div><br></div><div><br></div><div>Regards,</div><div><br></div><div>Anirban<br><br><div class="gmail_quote">On Thu, Sep 16, 2010 at 5:28 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div></div><div class="h5"><br>
<br>
Anirban Ghosh wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi ALL,<br>
<br>
I have carried out REMD simulation on a protein (20 replicas). Now I want to carry 2D PMF calculation using RMSD and Radius of gyration as the reaction coordinates using Grossfield Lab's WHAM package. For this what should be my input parameters to the WHAM program and in which format?<br>
Any suggestion in this regard is welcome.<br>
</blockquote>
<br></div></div>
I would suggest you consult the documentation for the program (i.e. the Grossfield WHAM manual, section 4.2.2). I don't know how you intend to pass your data to a program that is designed for umbrella sampling, but I suppose that's your task.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
Regards,<br>
<br>
<br>
Anirban<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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