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

[David van der Spoel]

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