NAMD electrostatic interaction Failure.

From: Mehran Bagheri (
Date: Wed Sep 25 2013 - 08:58:03 CDT

Dear NAMD users,

I was trying to calculate electrostatic interaction between two negative
and positive charged residues using NAMDEnergy plugin and I got -340
kCal/mol when there were close together. 340 kCal/mol is about 574 kT which
is huge. Then I found out, dielectric constant is 1.0 which is not correct
since I was not consider presence of water molecule. Searching
a little bit, I find out NAMD also use 1.0 since it also calculates water
molecule interaction. So my fist question is that

Is NAMD really use default value 1.0 for dielectric constant?

and if yes,
Does anyone try to examine this considering 1.0 for dielectric and
calculation water molecules will give one reasonable result or not?

I did actually, I calculated these two positive residue electrostatic
interaction with two negative residue as:

E(four residues with itself) - E(two positive with itself) - E(two negative
with itself) + E(four residues with water molecules)

However it give me even worse result?
So Any Idea how I can make this electrostatic interaction more reliable in
NAMD would be greatly appreciated?


ps : Switch is 10, Cutoff is 12

Mehran Bagheri
PhD. student of physics
Department of Physics
University of Ottawa
338A MacDonald Hall
150 Louis Pasteur
Ottawa, Ontario K1N 6N5
Phone:  +1 (613) 562-5800  ext. 2817
Email:  **

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