From: David Hardy (dhardy_at_ks.uiuc.edu)
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,
Dave
-- David J. Hardy, Ph.D. Theoretical and Computational Biophysics Beckman Institute, University of Illinois dhardy_at_ks.uiuc.edu http://www.ks.uiuc.edu/~dhardy/ > On Sep 11, 2017, at 7:20 PM, Michael LeVine <michaelvlevine_at_gmail.com> 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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