periodic boundary conditions in namd energy calculation

From: Lan Hua (lan.hua_at_gmail.com)
Date: Mon Nov 29 2010 - 15:52:43 CST

Dear NAMD users,

      I am wondering if the periodic boundary conditions have been applied
in the following calculation of interaction energy using namdenergy plugin
in VMD. It was done in text interface. The two atom selections are:

       set sel1 [atomselect top "resid 100 and water"]
       set sel2 [atomselect top "not (resid 100 and water)"]

The main options I specified are:
  -elec -vdw -sel $sel1 $sel2 -cutoff 12 -switch 10 -extsys *.xsc

I want to know whether the obtained vmd energy and the electrostatic energy
(with pme (-pme), or without) were calculated under the periodic boundary
conditions. Are the interactions between (resid 100 and water) and its
images included in the calculation?

    Thank you very much!!!

Lan

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