Hi,
A cutoff of 8.0 is the default in all Amber (not just pmemd.cuda) when
running PME calcs, and I disagree that this is too small. The PME
energies and forces themselves are independent of the cutoff size;
what it really affects is the van der Waals term, the effects of which
fall off quite rapidly with increasing distance. I think for PME it is
much more important to make sure your unit cell is large enough so
that your images aren't interacting with each other, i.e. there is
enough of a solvent buffer around your solute.
-Dan
On Fri, Jun 15, 2012 at 8:18 AM, Albert <mailmd2011.gmail.com> wrote:
> hello:
>
> I found that in the CUDA calculation the cut off always use 9.0 or
> even in most cases 8.0. I am curious about why it is so small? Is it
> because of the CUDA module or just because the developer would like to
> show a better performance of CUDA? Usually, from the literature in most
> cases, people use 10.0.
>
> THX
> Albert
>
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--
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Daniel R. Roe, PhD
Lab Specialist
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
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http://home.chpc.utah.edu/~cheatham/
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Received on Fri Jun 15 2012 - 06:30:03 PDT
