Re: Calculating Interaction Energies Using NAMD Energy Plugin

From: Peter Freddolino (
Date: Wed Jul 24 2019 - 13:23:51 CDT

Hi Joanna,
Quoting the namdenergy documentation,
"if only one selection is chosen, then internal energies for that selection
will be calculated, whereas if two selections are chosen, *only*
interaction energies between those selections will be calculated."
(emphasis added)

If you have two selections you will ONLY see the interaction energy between
the two groups, not the internal energies of each ligand. Keeping this in
mind, on what basis do you think the electrostatic energy is underestimated
in the pair case? (some numbers might be helpful)
The energy calculated for the interaction of two groups will often be quite
small relative to the internal energies of the participating groups
(especially if the ligands are some distance from each other).

On Wed, Jul 24, 2019 at 1:15 PM Joanna Zienkiewicz <> wrote:

> Hello all,
> I am trying to use the NAMD Energy plugin in VMD to calculate the
> interaction energies between two ligands during a course of MD
> trajectories. I have been doing this by choosing two atom selections (one
> for each ligand) but this seems to be giving me electrostatic energy values
> which are underestimated to a great extent. When I group both ligands
> together into a single selection and calculate the internal energies,
> however, the electrostatic values are much more reasonable.
> Does anyone have any ideas why NAMD Energy is behaving this way?
> Thank you for any suggestions,
> Joanna Zienkiewicz

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