From: Chris Chipot (chipot_at_ks.uiuc.edu)
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
_______________________________________________________________________
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
E-mail: chipot_at_ks.uiuc.edu
Christophe.Chipot_at_edam.uhp-nancy.fr
Web: http://www.ks.uiuc.edu
http://www.edam.uhp-nancy.fr
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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