Re: NAMD electrostatic interaction Failure.

From: Kenno Vanommeslaeghe (
Date: Wed Sep 25 2013 - 19:32:11 CDT

I'm not sure I understand your post correctly, but you seem to be a bit
confused about the physics of what you're doing. I'd recommend reading
some literature and textbooks; see for instance

To answer your question, if the interaction energy is that high, the
residues have to be so close together that there cannot be any water
molecules between them, so then the dielectric constant of 1 is correct,
and your (potential) energy seems to be *roughly* in the right ballpark
for 2 salt bridges. That said, it is indeed disconnected from most
real-life observables, not because of the dielectric constant, but because
said observables are typically related to *free* energy *differences*
between the bound state and a *solvated* reference state (the solvation
free energy for ions is huge). How to approximate such free energy
differences is not a trivial question and there exists a large body of
literature on this subject, and and a large number of methods.

Oh yeah, for the case of the residues being further apart, there are
explicit and implicit water models. Setting the dielectric constant to
anything other than 1 is not a common practice anymore these days (though
it still has niche applications), so the default of 1 is entirely reasonable.

On 09/25/2013 09:58 AM, Mehran Bagheri wrote:
> 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?
> Mehran
> 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
> Canada
> Phone: +1 (613) 562-5800 ext. 2817
> Email: <>_
> :MB

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:47 CST