<div>Thank you guys! So, is there any tutorial in Gromacs for calculating free energy of ligand binding using FEP?</div>
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<div>Steven<br><br></div>
<div class="gmail_quote">On Mon, Oct 10, 2011 at 2:02 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="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im"><br><br>mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi<br>Please have a look at Dr.Justin tutorial page at the following link:<br><br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin/<u></u>gmx-tutorials/index.html</a><br>
<br></blockquote><br></div>This tutorial is not for FEP explicitly, but may be of some use. There is discussion on using the BAR algorithm for binding free energy calculations.<br><br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Cheers
<div class="im"><br><br>On Mon, Oct 10, 2011 at 12:27 PM, Steven Neumann <<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a> <mailto:<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>><u></u>> wrote:<br>
<br> Hi Gmx Users,<br> Can you suggest some reading and some tutorial in calculations of<br> binding free energy (ligand binding) in Gromacs? ?I want to use Free<br> Energy Perturbation method.<br> Steven<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" target="_blank" value="+15402319080">(540) 231-9080</a><br>
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