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

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
>
> _______________________________________________________________________
>
> Chris Chipot, Ph.D.
> on leave from Nancy Universit®¶, CNRS
> Theoretical and Computational Biophysics Group
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>
> E-mail: chipot_at_ks.uiuc.edu
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>
> I disapprove of what you say, but I will defend to the death your right
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> Evelyn Beatrice Hall
> _______________________________________________________________________
>

-- 
Roman Petrenko
Physics Department
University of Cincinnati

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