On Fri, Aug 16, 2002, mer_at_gordon.chem.wayne.edu wrote:
Please send questions about running Amber to the Amber reflector, not
to me personally. That way, many people can have a chance to see your
questions and the replies.
> The reason I am asking whether I can use sander to run PMF is that
> our system is very large and gibbs cannot be used to run in parallel.
> Are you aware of whether the PMF option in Charmm runs in parallel?
> Also, do you have any recommendation on what type of histograming
> technique would be best (perhaps literature from AMBER developers on
> this issue)? We are hoping to get a free energy profile for rotation
> about two bonds.
The "standard" histogramming method is called WHAM ("weighted histogram
analysis method"). Standard references are:
%A S. Kumar
%A D. Bouzida
%A R.H. Swendsen
%A P.A. Kollman
%A J.M. Rosenberg
%T The weighted histogram analysis method for free-energy calculations
on biomolecules. I. The method.
%J J. Computat. Chem.
%V 13
%P 1011-1021
%D 1992
%A S. Kumar
%A J.M. Rosenberg
%A D. Bouzida
%A R.H. Swendsen
%A P.A. Kollman
%T Multidimensional free-energy calculations using the weighted histogram
analysis method
%J J. Computat. Chem.
%V 16
%P 1339-1350
%D 1995
..good luck...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Fri Aug 16 2002 - 12:23:16 PDT
