From: dhacademic (dhacademic_at_gmail.com)
Date: Sun Nov 14 2010 - 09:51:40 CST
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 (
http://www.ks.uiuc.edu/Research/namd/2.7/ug/node23.html). 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.
Any suggestion is appreciated,
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