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

From: Chris Chipot (
Date: Wed May 13 2009 - 18:16:54 CDT

Because the dual-topology paradigm is implemented pretty deep in
the code, at the level of the non-bonded forces, with multiple
PME grids for incoming-outgoing particles, this feature will not
work in the Cuda-version. The latter can, however, be used as an
MD engine to generate configurations at λ, to which perturbation
theory can be applied by means of external scripting.


Axel Kohlmeyer wrote:
> On Wed, 2009-05-13 at 18:00 -0400, Roman Petrenko wrote:
>> By the way, is fep implemented in cuda-version of namd?
> check out.
> NAMD currently puts only the most time consuming part of the
> calculation on the GPU (non-bonded forces) so the rest should
> just work as is without any special requirements.
> cheers,
> axel.


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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to say it
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