[gmx-users] Free energy landscape by g_sham

[David van der Spoel]

On 2013-03-31 12:21, Kavyashree M wrote:
> Thank you Sir

Note that the free energy differences are rigorously correct only if the 
array of the cells in the grid correspond units of phase space with the 
same volume. This is close to impossible to achieve, but the plots may 
still give insight.
>
> 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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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se