[AMBER-Developers] vdW radii in pmemd.cuda

From: David A Case <case.biomaps.rutgers.edu>
Date: Wed, 1 Aug 2012 10:16:50 -0400

On Mon, Jul 30, 2012, Jason Swails wrote:
> Actually, pmemd.cuda automatically applies a value of 0.5 angstroms as
> the sigma value (or epsilon? I always get those confused) for atoms
> whose vdw parameters are 0 and we've seen no ill effects so far (and the
> code gets tested pretty thoroughly).

(Expresses surprise!) Is this documented anywhere? What value of epsilon is
used? Since Amber inputs never use sigma, is it Rmin that is set to 0.5 Ang?)
Aside from not seeing "ill effects" has anyone done careful testing?
For example, are the properties of TIP4P water (etc.) really unchanged?


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Received on Wed Aug 01 2012 - 07:30:02 PDT
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