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
