pair interaction calculations

From: dhacademic (
Date: Sun Nov 14 2010 - 09:51:40 CST

Hi Everyone,

I want to calculate the interaction energy between two groups. The following
configuration file is used for the pair interaction calculation, and only
non-bonded terms are calculated. To make sure that the calculation is
correct, I also manually calculate the ELECT and VDW according to the
potential energy functions of namd ( The system is very
simple, which only contains two Cl- (qi=qj=-1) with the distance of 3.57
angstrom (rij=3.57) in gas phase.

The results from the the following configuration file is 84.9920 (ELECT)
and 1.4148 (VDW). I can well reproduce the VDW result by manual calculation.
However, my manually calculated ELECT is 92.98, which is quite different
from the above result.

structure mycl.psf
paraTypeCharmm on
parameters par_all27_prot_lipid.prm
numsteps 1
exclude scaled1-4
outputname pair
temperature 0
COMmotion yes
cutoff 17
pairlistdist 18.5
dielectric 1.0
switchdist 15
pairInteraction on
pairInteractionGroup1 1
pairInteractionGroup2 2
pairInteractionFile mycl.pdb
pairInteractionSelf off
coordinates mycl.pdb
run 0

Any suggestion is appreciated,


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