namd energy self interaction reality check

From: Thomas C. Bishop (
Date: Mon Nov 24 2008 - 23:38:51 CST

Greetings namd,
I'm using namd to calculate energies from an existing trajectory w/ the
tcl scripting capabilities.

I am only calculating "self interaction energy" for a group of atoms
that's w/in a bubble of radius 30A.

I expect that once the cutoff is large enough to include all atoms in
my group (30A bubble) that the electrostatic and vdw energies won't
change as a function of cutoff...

But this is not happening. the vdw and elec energy changes up to a
cutoff of over 100A... bond,angle,dihed remain constant as function
cutoff for any given snapshot (as expected)

here's relevant section of my namd.conf file.
I've run the calcs w/ cutoff from 8A up to 100A and elec and vdw
continues to change... but the atoms in my system are all w/in 30A of
each other..I thought after 30A nothing would change.

what am I missing? (i've checked that the group is really the group I
think it is)

it's late hopefully someone will provide an answer by morning...
final note PME is off so it's not a size scaling effect.

thanks for any insight/input.


margin 2.0
switching on
switchdist 8.0
cutoff 10.0
pairlistdist 12.0

pairInteraction on
pairInteractionCol B
pairInteractionSelf on
pairInteractionGroup1 1
pairInteractionFile select.pdb

*  Thomas C. Bishop   *
*Office: 504-862-3370 *
*CCS:    504-862-8391 *
*Fax:    504-862-8392 *

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