colvar for PMF calculation

From: Navendu bhatnagar (
Date: Tue Apr 20 2010 - 18:02:28 CDT


This mail is regarding the use of COLVAR module for PMF calculations in

I have performed protein-lipid interaction MD simulations using NAMD engine
and as a part of analysis, I need to calculate the PMF
of these interactions. The way this will be done is by performing a set of
calculations for varied distances
 along a reaction coordinate which is a vector between the center of mass of
protein and the bilayer in the 'z'-direction (normal to the bilayer surface)

The bilayer and protein backbone shall be constrained using a spring
constant and the restraint forces will be evaluated at every stage.

My question here is that does SMD COLVAR method supports this kind of
calculation ?
The reason I ask is because I need a restraint force as output but I don't
see that option in the COLVAR documentation in NAMD user guide.


Deptt. of Chemical Engineering

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