Thank you Sir Regards kavya
On Sun, Mar 31, 2013 at 11:58 AM, bipin singh <bipinel...@gmail.com> wrote: > g_sham calculates free energy landscapes by computing the joint > probability distribution from the two dimensional plane constructed > using two quantities (in your case it will be rmsd and radius of > gyration). Conformations sampled during the simulation were projected > on this two dimensional plane, and the number of points occupied by > each cell was counted. The grid cell containing the maximum number of > points is then assigned as the reference cell, with a free energy > value of zero. Free energies for all the other cells were assigned > with respect to this reference cell using the following equation: > > ΔG = -kbT ln P(x,y)/Pmin > > P(x,y) is the estimate of probability density function obtained from a > histogram of MD data and Pmin is the maximum of the probability > density function. Kb is the Boltzmann constant, and T is the > temperature corresponding to each simulation. > > > On Sun, Mar 31, 2013 at 10:35 AM, Kavyashree M <hmkv...@gmail.com> wrote: > > Dear users, > > > > > > Can someone kindly explain how g_sham calculates > > the free energy landscape of given two quantities say, > > rmsd and radius of gyration. > > Any references are welcome. > > > > Thank you > > with Regards > > Kavya > > -- > > 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 > > > > -- > ----------------------- > Thanks and Regards, > Bipin Singh > -- > 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
