H = U +pV, all these terms are available through g_energy. Your resulting values will be per mole, so I would perform no additional normalization.
Personally, I would simulate all cases (folded, unfolded, etc) with the same number of waters -- to avoid any possible artifacts. Dr. Vitaly V. Chaban On Mon, Jul 15, 2013 at 9:34 AM, <pooja_gu...@nccs.res.in> wrote: > Thanks Vitaly > > but how?? > > let's say the difference between unfolded to folded protein is 100 water > molecules. What is the correct procedure to calculate (theoretically) the > entrapy correspond to single water molecule for stabilizing/destabilizing > the protein. > > help me > > > Sure, you can. > > > > > > > > Dr. Vitaly V. Chaban > > > > > > On Mon, Jul 15, 2013 at 8:38 AM, <pooja_gu...@nccs.res.in> wrote: > > > >> Hi > >> > >> I want calculate the enthalpy of water molecule corresponding to protein > >> folded and unfolded state. > >> How much a single water molecule (enthalpy and free energy) contribute > >> in > >> folding ? > >> Can we calculate enthapy from g_energy? > >> > >> > >> > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> * Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists