[gmx-users] Free energy landscape by g_sham

[bipin singh]

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 <hmkvsri at 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 at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



-- 
-----------------------
Thanks and Regards,
Bipin Singh