Dear Shahab<br><br>You need to do one of the following methods;<br>1-Umbrella Sampling and computing PMF curve<br>2-Thermodynamic Integration<br><br>Please read some tutorials by Dr.Justin ,<br>It can be very useful<br><br>
Be success<br><br><div class="gmail_quote">On Tue, May 17, 2011 at 3:08 PM, shahab shariati <span dir="ltr"><<a href="mailto:shahab.shariati@gmail.com">shahab.shariati@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear gromacs users<br><br><br>my simulation system is protein-ligand.<br><br>I did 3 simulations. protein only, ligand only and protein-ligand complex.<br><br>I want to know how to obtain binding energy between protein and ligand by MD simulation using gromacs.<br>
<br><br>any help will highly appreciated.<br>
<br>--<br>
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