From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Wed May 13 2009 - 17:45:29 CDT
Thanks for reply,
as i understand such external scripts one has to write by himself, right?
On Wed, May 13, 2009 at 6:37 PM, Chris Chipot <chipot_at_ks.uiuc.edu> wrote:
>> 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(¶ň), modify your parameters
> and calculate U(¶ň+¶ń¶ň), 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 ¶ň.
> Chris Chipot, Ph.D.
> on leave from Nancy Universit®¶, 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
> Web: http://www.ks.uiuc.edu
> I disapprove of what you say, but I will defend to the death your right
> to say it
> Evelyn Beatrice Hall
-- Roman Petrenko Physics Department University of Cincinnati
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