[gmx-users] how to find conformational free energy?

David van der Spoel spoel at xray.bmc.uu.se
Fri Apr 3 11:00:12 CEST 2009

ajani haresh wrote:
> can anyone tell me how to find the conformational free energy?
> i have the one peptide which have 12 amino residue.
> i was run the simulation. and found the g_energy from trajectory file.
> i have potential energy.
> now i want to find the conformational free energy and entropy and enthalpy.
> any one know plz help me.
> thanks...
You can estimate the conformational entropy using g_covar and g_anaeig 
(Quasi-harmonic and Schlitter). You probably need to do some literature 
search as well, these are difficult topics.

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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