<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Anirban,</div><div><br></div><div>You *could* use the configurations in your trajectory to (re)calculate average energies; by de-coupling your ligand this would get you the average free energy change per coupling strength change at the point where the ligand is fully bound.</div><div><br></div><div>If you're interested in free energy of binding, and want to use a correct free energy method, you'll probably need to do at least 10 simulations between your system with the ligands bound, and a version of your system with the ligand not bound to the protein - just to correctly sample the mutually accessible phase space between those two states. </div><div><br></div><div>These calculations are decidedly non-trivial, though, and I'd recommend reading up on how to do these things in Frenkel&Smit ('Understanding molecular simulations'), for example.</div><div><br></div><div>Sander</div><div><br></div><div><br></div><br><div><div>On 22 Mar 2010, at 07:07 , Anirban Ghosh wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div class="gmail_quote"><br>Hi ALL,<div><br></div><div>I have run a protein + ligand simulation using GROMACS4.0.7. I want to do a free energy calculation now. However, in my mdrun option I did not use the -dgdl option, nor I have used free_energy=yes in the MDP file (as I was not sure that I will be calculating free energy later). How can I now calculate the free energy? g_lie does calculate free energy, but the archives are telling its not very accurate. Is there any other way to do it? Can g_energy be used somehow? Any suggestion is welcome. Thanks a lot in advance.</div>
<div><br></div><div>Regards,</div><div><br></div><font color="#888888"><div>Anirban</div>
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