[gmx-users] Free energy landscape by g_sham

[Kavyashree M]

Thank you Sir

Regards
kavya


On Sun, Mar 31, 2013 at 11:58 AM, bipin singh <bipinelmat at 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 <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
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>
> --
> -----------------------
> Thanks and Regards,
> Bipin Singh
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