On Thu, Aug 2, 2012 at 10:01 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Wed, Aug 01, 2012, Jason Swails wrote:
> >
> > Hmm... looking into this more, this may be a slightly false alarm. Rmin
> > (or sigma, as it's called in the CUDA code) is set to 0.5, but epsilon is
> > still set to 0.
>
> Just to remove uncertainty: Rmin and sigma are different quantities; the
> variable called "sigma" in gpu.cpp is indeed sigma. The *input* variable
> in
> Amber force fields is Rmin. See
> http://ambermd.org/Questions/vdwequation.pdf.
>
So it is, not sure how I missed that first eqn... but combined Lennard
Jones terms with sigma_i = 0.5 and epsilon_i = 0 will still be 0 it
appears. In which case, setting sigma=0.5 vs. 0 has no effect on HO and HW
types, although perhaps slightly misleading.
Thanks,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Aug 02 2012 - 07:30:05 PDT
