Re: Amber topology in CUDA NAMD - can it be done?

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Oct 19 2010 - 11:43:10 CDT

Thanks for the explanation. NBFIX support is on the list for the next
version of the CUDA nonbonded kernel, but I don't know how or by when it
will be done and what the performance impact will be.

-Jim

On Tue, 19 Oct 2010, Axel Kohlmeyer wrote:

>>
>> none that i know. the NBFIX error is a bit of a misnomer.
>
> perhaps i should add an explanation where NBFIX is used in CHARMM, too.
>
> NBFIX is a section in a CHARMM parameter file. it is rather small
> and mostly covers non- bonded parameter overrides for "strange"
> entities like divalent cations, which are near impossible to model
> well with a simple pairwise additive potential in the first place.
>
> cheers,
> axel.
>
> --
> Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>

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