pair interaction cutoff

From: Holly Freedman (
Date: Mon Aug 21 2006 - 21:51:30 CDT

Hi NAMD user help,

I have been working on the problem of calculating the solute-solvent interaction energy from the pair
interaction module of NAMD, and I have the following question please. Is it possible to clue namd to do
the cutoff for the energy calculation in such a way so that the hydrogens on the waters stay together
with the oxygens, that is they only get cutoff if the oxygens are and vice versa? I am running periodic,
without PME, trying to use a cutoff of about 9 to 11 Angstroms.

Thanks in advance
Holly Freedman

Department of Physics, University of Alberta
Edmonton CANADA

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