From: Michael LeVine (
Date: Tue Sep 12 2017 - 09:37:30 CDT

Hi all,

I am calculating the non-bonded interaction energy between an ion and its
coordinating residues over the course of a simulation using the NAMD Energy
Plug-in. While NAMD Energy has the option to use PME in the calculation,
which we used during our simulations, it is not clear to me how the plug-in
is calculating the portion of the long-range electrostatic interaction. It
is my understanding that once using PME, the long-range electrostatic terms
can't be trivially decomposed. Is the plug-in only outputting the
short-range interaction terms?



Michael V. LeVine, PhD
Institute Fellow, Institute for Computational Medicine
Instructor in Physiology and Biophysics
Instructor in Computational Biomedicine
Department of Physiology and Biophysics, Weill Cornell Medicine