Calculating Interaction Energies Using NAMD Energy Plugin

From: Joanna Zienkiewicz (
Date: Wed Jul 24 2019 - 11:41:58 CDT

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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