Re: PMF calculation using fixed restraints

From: Chris Chipot (
Date: Sun Nov 06 2005 - 14:54:16 CST

The easiest way is to use the adaptive biasing force (ABF) method
available in version 2.6. Details about this method can be found
in the user's manual, along with examples. There is no need to
worry about fixed restraints, nor constraints. Simply define the
reaction coordinate as the distance separating the COM of your

Chris Chipot

Vani Krishna wrote:

>I would like to calculate the Potential of Mean force
>between two solute molecules in water. I was thinking
>of using fixed restraints and change the distance
>between the center of masses of the two molecules from
>4-12 A (1 A step)and compute PMF.
>so my question is how do I go about it in NAMD? I saw
>in the manual about the fixed restaints. but can any
>one send me a cript of how to compute PMF using fixed
>restraints in NAMD?

Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Université Henri Poincaré - Nancy 1 Phone: (33) 3-83-68-40-97
B.P. 239 Fax: (33) 3-83-68-43-87
54506 Vandœuvre-lès-Nancy Cedex


      To sin by silence when we should protest makes cowards out of men
                                                    Ella Wheeler Wilcox

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