Re: namd 2.7b: measure free energy difference "growing" a force constant

From: Chris Chipot (
Date: Sat Jun 20 2009 - 10:07:16 CDT


there are currently /no/ substitute to the old thermodynamic-integration
based module for the function that you describe - namely estimating the
free-energy change due to an appearing or a disappearing restraint.

FEP only handles alterations of a topology, while ABF/MtD within Colvars
is the appropriate toolkit for free-energy landscapes along geometrical,
collective variables.

Ability to /grow/ or /shrink/ the force constant is, however, a useful
feature when one wants to measure the free-energy contribution due to
losses of configurational entropy in /absolute/ binding affinity

The old thermodynamic-integration based module is still working in 2.7,
albeit no longer documented. We are currently thinking of alternatives,
either within the FEP or the Colvars framework.


Sebastian Stolzenberg a écrit :
> Dear All,
> sorry I might have missed this piece of info:
> In namd 2.6, with the old PMF module (manual, p. 87), I could measure
> free energy differences, "growing" a force constant on a particular
> restraint.
> In namd 2.7b, what module can I use instead to have full support again?
> ABF in the colvar? ... how :) ?
> Thank you,
> Sebastian


Chris Chipot, Ph.D.
on leave from Nancy Université, CNRS
Theoretical and Computational Biophysics Group
Beckman Institute
University of Illinois at Urbana-Champaign
405 North Mathews Phone: (217) 244-5711
Urbana, Illinois 61801 Fax: (217) 244-6078


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