Dear Justin<div>Thank you very much for your prompt reply. I have read about your Perl scripts. Kindly, would you please let me know where did you exactly set that Lambda must increase from 0 to 1 by increment of 0.05? which parameter in your energy stuff stating that Lambda must increase by 0.05 in every step? </div>
<div>Best regards</div><div>Meisam</div><div><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Message: 3<br>
Date: Tue, 27 Sep 2011 13:38:54 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Re: problem in binding free energy<br>
calculation and setting Lambda<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E820A2E.30501@vt.edu">4E820A2E.30501@vt.edu</a>><br>
Content-Type: text/plain; charset=windows-1252; format=flowed<br>
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meisam valizadeh kiamahalleh wrote:<br>
> Dear Marcelo<br>
><br>
> Thank you very much for you kind reply.<br>
> Actually, I am following Justin Lemuk's tutorial. He used pear script to<br>
> do all simulations in one setting. Unlike him, I want to do each one<br>
> separately and unfortunately, I couldn't get any info for my second<br>
> question which is about setting initial and final Lambda for my energy<br>
> stuff in each simulation. Could you please help me which parameters I<br>
> need to change for each step?<br>
<br>
The Perl scripts write the files you need to complete the tutorial. You can<br>
then run as many of the resulting Bash scripts to execute the simulation(s) for<br>
individual lambda values. The theoretical background is all explained in the<br>
tutorial. You need to do a transformation between lambda = 0 and lambda = 1,<br>
with sufficient intermediate values to get good overlap of the free energy<br>
histograms (also explained in the tutorial).<br>
<br>
-Justin<br>
<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> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><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>
<br>
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