Pair interaction, PBC included?

From: Edward Patrick Obrien (
Date: Sat Nov 20 2004 - 14:22:39 CST

Hi all,
  I have a question, which is probably relevant to previous discussions on
binding energies.

Question 1:
  Does the "Pairinteraction" function use periodic boundaries in
calculating the energies?
  In the example NAMD configuration files which implement this function I
see no parameters defined for PBC.

  It seems that if it doesn't include PBC you could get erroneous results
for your non-bonded interaction energies (since a molecule could be near a
periodic boundary but wouldn't interact with the particles right next to
it in the image cell).

Question 2:
  After running a "pairinteraction" analysis, does the output containing
the total energy consist of only the Vdw and elec interaction energies?
If so, then Einteraction should equal Etotal in the output. Or is it not
that straightforward?

Any thoughts, comments, would be appreciated.

PS- The reason I bring this up is I want to calculate the energetic
interactions associated with a sidechain and the rest of the system.

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