Re: pairInteraction and PME?

From: David Hardy (
Date: Tue Sep 12 2017 - 11:05:23 CDT

Hi Michael,

When evaluating with pairInteraction, NAMD evaluates the long-range gridded part for PME three times, once for the atoms in set A, once for the atoms in set B, and once for the atoms in sets A and B together, then it calculates differences to determine the long-range interaction forces and energy between the A and B sets of atoms. The short-range interactions between sets A and B are calculated in the obvious way.

Best regards,

David J. Hardy, Ph.D.
Theoretical and Computational Biophysics
Beckman Institute, University of Illinois
> On Sep 11, 2017, at 7:20 PM, Michael LeVine <> wrote:
> Hi all,
> When pairInteraction is used to calculate the interaction between two groups of atoms with PME, how do the long-range interactions contribute? It is my understanding that once using PME, the long-range electrostatic terms can't be trivially decomposed. Does pairInteraction only output the short-range terms, or also include the total long-range electrostatics (and thus both between and within group)? 
> 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

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