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?
Thanks,
Ignacio
On Fri, Jul 29, 2011 at 10:44 AM, case <case.biomaps.rutgers.edu> wrote:
> On Fri, Jul 29, 2011, Ignacio J. General wrote:
>>
>> 1) Does EELEC include the whole Ewald energy of the system, that is
>> including 1-2, 1-3 and 1-4 interactions?
>
> No. Amber always ignores 1-2 and 1-3 interactions, and scales 1-4
> interacctions.
>
>> 2) Is 1-4EEL the negative of the 1-4 interactions, not including 1-2 and 1-3?
>
> No. The sum of all the electrostatic interactions that Amber considers (see
> point 1 above) is 1-4EEL + EELEC.
>
> ....dac
>
>
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Received on Fri Jul 29 2011 - 08:00:05 PDT
