RE: cut-off question

From: case <>
Date: Fri 6 Sep 2002 17:01:28 -0700

>===== Original Message From Cozmuta <> =====
> What should be the correct way to decide what cutoff to
>use when one does not use PBC?

I don't think there is any "good" answer here. If you can afford no
cutoff, that should be the most reliable. There is a large literature
on selecting cutoffs, but the answer really depends upon what use you wish
to make of the results. For some things, no cutoff scheme will work well
(such as quantities depending upon absolute electrostatic energies, and
probably even for such energy differences. Other more qualitative
investigations may not suffer so much.

The "win" with PBC and PME is that it is both cheaper and better than cutoff
schemes. As I have said here before, "good" schemes for droplet simulations
(using reaction fields or similar boundary conditions) have not yet been
implemented in Amber.

...hope this helps....dac

David A. Case | e-mail:
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA |
Received on Fri Sep 06 2002 - 17:01:28 PDT
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