[gmx-users] PMF's

David L. Bostick dbostick at physics.unc.edu
Wed Nov 19 23:31:01 CET 2003

Hi Ilya,

How do you mean? ... If you have adequate sampling along the degree of
freedom over which you wish to calculate the PMF, it is easily done .. Say,
for example the coordinate is z. Then ,

PMF(z) = -kT log(P(z)), where P(z) is the probability (or normalized
density) along the coordinate.

But if you do not have adequate sampling along z, you must devise a way to
sample it.  Then you must look into free energy methods, such as umbrella
sampling, monitoring the constraint force along z and then integrating it,
or thermodynamic integration at points along the reaction path, etc....


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick

On 19 Nov 2003, Ilya Chorny wrote:

> Has anyone attempted to calculate PMF's by freezing the movement along
> two dimensions and allowing movement along one dimension?
> Ilya
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