PMF calculation using fixed restraints

From: Vani Krishna (
Date: Sun Nov 06 2005 - 12:26:22 CST


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?


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