Subject: How to calculate PMF between two solute molecule in a MD simulation.

From: Niharendu.Choudhury[at]mail.uh.edu
Date: Thu, 09 Oct 2003 14:01:52 -0500 (CDT)

Dear CCLers,
I have a system of two solute atoms in a solvent and I am running MD for various
fixed distances (r_0) between two solute atoms.
Can anybody tell me in details how to calculate the PMF between these two solute molecules using say Free endrgy Perturbation method.

Is there any code available which can be directly added to my MD code.
It will be helpful if anybody let me know any literature which describes these methods in details.

Thanks in advance
Niharendu Choudhury