Re: PMF with sander module

From: David A. Case <>
Date: Fri 16 Aug 2002 12:23:16 -0700

On Fri, Aug 16, 2002, 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:
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            |
Received on Fri Aug 16 2002 - 12:23:16 PDT
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