ichorny at maxwell.compbio.ucsf.edu
Thu Nov 20 00:36:01 CET 2003
I'm less concerned about the sampling and more about the affect on
freezing movement in two of the dimensions. How removing those
contributions will effect the results.
On Wed, 2003-11-19 at 14:30, David L. Bostick wrote:
> 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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