Re: collective variable space PMF, including biasing potential terms?

From: Chris Chipot (
Date: Wed May 13 2009 - 17:37:04 CDT

> By the way, is fep implemented in cuda-version of namd?

In short, no. For the time being, external scripting might be
advisable, whereby you loop over the configurations generated
by your Namd-cuda run, calculate U(λ), modify your parameters
and calculate U(λ+δλ), prior to averaging. This is tantamount
to a single-topology-like paradigm. A properly written script
may give you the illusion of estimating the free-energy change
on the fly, the main computational effort being the generation
of the ensemble of configurations at λ.



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


I disapprove of what you say, but I will defend to the death your right
to say it
                                                    Evelyn Beatrice Hall

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