[gmx-users] Free Energy Calculation

Sander Pronk pronk at cbr.su.se
Mon Mar 22 10:56:02 CET 2010

Hi Anirban,

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.

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. 

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.


On 22 Mar 2010, at 07:07 , Anirban Ghosh wrote:

> Hi ALL,
> 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.
> Regards,
> Anirban
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100322/d4b86507/attachment.html>

More information about the gromacs.org_gmx-users mailing list