On Fri, Jul 29, 2011, Ignacio J. General wrote:
> OK, that is clear now. But I have a last question. As far as I know,
> in the Ewald equations it is not possible to ignore, say, 1-2
> interactions without also ignoring 1-2', 1-2'', etc. interactions
> (where the primes represent the copies of atom 2 in other cells). In
> general, the effect of 1-2', 1-2'', ... is pretty small when compared
> to 1-2, so it should be a good approximation. Is that what Amber does,
> or is there some other way of ignoring 1-2 without ignoring 1-2', etc?
Briefly (see the implementation papers for details): the reciprocal part of
the PME calculation includes all interactions. After this, the reciprocal
part of the 1-2 interaction is subtracted (in a sum over 1-2 interactions).
Hence 1-2' interactions *are* a part of the total energy, but 1-2
interactions are excluded.
....dac
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Received on Fri Jul 29 2011 - 09:00:03 PDT
