Re: PMF with sander module

From: Pratul Agarwal <>
Date: Wed 14 Aug 2002 20:49:34 -0700 (PDT)

The section 7.8.5 of AMBER 7.0 manual (or section 9.8.5 in AMBER 6.0)
explains how some of the PMF calculations can be carried out using
gibbs module. Maybe this is more appropriate if you want to use the
thermodynamic integration approach.

If you really want to use the sander module, you can use "umbrella
sampling" technique by applying the restraints manually (see section
5.9 of the manual for AMBER v7.0 or section 6.10 in AMBER v 6.0). You
will then have to use some histogramming technique on the data
collected to generate the PMF curve.

Good Luck.

--- "> wrote:
> Dear amber users:
> Could the thermodynamic integration option in sander be used to
> carry out potential of mean force calculations?
> Thanks, Samy.
> --
> -----

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Received on Wed Aug 14 2002 - 20:49:34 PDT
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