From: John Stone (
Date: Wed Sep 13 2017 - 11:51:55 CDT

  The NAMD Energy plugin is largely just a simple graphical interface
that generates the necessary NAMD config file to perform the requested
calculations by re-running NAMD on a trajectory file. The plugin itself
mostly just communicates with NAMD which does all of the work since as
you point out, it would be impossible to separate different force/energy
contributions ex post facto, so these are calculations that have to be
done inside of NAMD itself.

  John Stone

On Tue, Sep 12, 2017 at 02:37:30PM +0000, Michael LeVine wrote:
> 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?
> Thanks,
> Michael
> --
> 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

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349