Avoiding self-interaction with PME.

From: Niels Christensen (nielsjchristensen_at_gmail.com)
Date: Sun Nov 25 2007 - 09:59:57 CST

Dear NAMDers.

It is clear that self-interaction, in the case where electrostatic
interactions are truncated at the cutoff, can be easily prevented by
choosing the amount of padding around the protein in each direction to be
slightly larger than half the cutoff. With such a set-up, it is guaranteed
(given NVT and size-constant protein) that self-interaction is absent
throughout the entire simulation run. But what if I decide to use employ
full electrostatics via PME? In this case, how should I produce a reliable
estimate of the amount of (water) padding required to avoid

Any suggestions are highly appreciated.

Best regards
Niels Christensen

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