Re: NAMD energy plugin

From: Aron Broom (
Date: Wed Jun 04 2014 - 13:34:51 CDT

you might need to give some more details about what precisely you asked the
plugin to do.

While I don't know anything about the plugin, if I were to guess what it
did, is that it took all the atoms in Glu and calculated the pairwise
interactions with all the atoms in the ligand. So your electrostatic term
should be bigger than an H-bond, because it's more than just one pair of
atoms interacting.

Also, if you are comparing that number to anything to see how reasonable it
is, you have two problems:

1) This is just an enthalpy, there is no entropy. Binding between
molecules is generally weak (a few kcal/mol) but the individual enthalpy
(H) or entropy (TS) terms are usually much higher, but tend to cancel one
another out.
2) Even if you are just comparing to an enthalpy, this is still just a raw
enthalpy, that is, an H and not a delta-H which is the kind of value you
would get from an experiment since raw enthalpies are not measurable. So
you'd need to compare your enthalpy to some reasonable reference, like the
ligand in water or something.

On Wed, Jun 4, 2014 at 1:45 PM, Ramin Ekhteiari <>

> Hi dears,
> I am trying to calculate energy between one polar amino acid residue (GLU)
> and a small ligand using NAMD energy plugin during a course of MD
> trajectories, but I face with results as below, (the electrostatic
> energy values are not reasonable for a H-bond).
> Frame Time Elec VdW Nonbond
> Total
> 0 0 -105.632 -3.0657 -108.698
> -108.698
> 1 1 -103.383 -3.9904 -107.373
> -107.373
> Would be grateful for any comments,
> Cheers,
> Ramin.

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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