compute nonbonding interactions on bonded atoms

From: Lorant Janosi (
Date: Fri Dec 29 2006 - 23:10:12 CST


My question is the following:
I am trying to modify namd code so that it will calculate nonbonded
interactions on atoms that are bonded - as far as I know, namd does not
calculate any nonbonding interactions on atoms that have some kind of
bonded interaction (e.g. ComputeHomeTuples like). But I can't seem to
find where the atoms are tested for these bondings and excluded from the
nonbonding interaction list. Can anyone help me with this?
Thank you very much.

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