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Message: 1<br>
Date: Tue, 05 Jul 2011 19:14:04 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] free energy calculations<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:4E139ABC.1030107@vt.edu">4E139ABC.1030107@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
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Ragothaman Yennamalli wrote:<br>
> Hi,<br>
> I want to run free energy calculations on a particular protein-ligand<br>
> complex. I do not have much knowledge on this so I have some questions,<br>
> hopefully someone might give me clear answers.<br>
> I am following the tutorial given in this link:<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html</a><br>
><br>
> My questions are as follows:<br>
> 1. I am assuming that I do not need the "protein without the ligand"<br>
> form for free energy calculations. Am I right?<br>
><br>
<br>
Free energy calculations can be done on a number of systems. The tutorial is<br>
just one simple example.<br></blockquote><div><br>Thanks for the mail. So, I technically do not need both the un-complexed and complexed form of the protein with the ligand. <br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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> 2. To use g_bar, I need to run the protein-ligand complex with<br>
> a) first with lambda ranging from 0.5 to 1 for vdw coupling and<br>
> b) followed by lambda ranging from 0.5 to 1 for coulombic coupling<br>
> Adding these would give the deltaG I am looking for. Am I right?<br>
><br>
<br>
No. The range for lambda should be 0 to 1. Using 0.5 to 1 gives only part of<br>
the free energy for the transformation, and not necessarily half.<br></blockquote><div><br>Apologies, I should have mentioned as from 0 to 1. So, the first step is to do vdw coupling followed by coulombic coupling. Right?<br>
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> 3. Are there any papers that use g_bar function in gromacs to calculate<br>
> free energy?<br>
><br>
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The g_bar tool is relatively new to Gromacs, so maybe not. The BAR method<br>
itself has been around for decades though, so its applications have been<br>
demonstrated in the literature many times.<br></blockquote><div><br>Thanks for pointing this.<br>Raghu <br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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-Justin<br>
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--<br>
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<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>
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