[AMBER] Bug in LIE action command of cpptraj?

From: Samuel Bowerman <sbowerma+amber-l.hawk.iit.edu>
Date: Wed, 27 May 2015 14:25:27 -0500

Hello Amber community,

I believe there may be a bug in the way that the "lie" action command of
cpptraj calculates electrostatic interactions. It appears that the command
divides the individual elements of the charge matrix by the defined
dielectric value and then uses these "new" charges to calculate
electrostatic interactions. However, in doing so, isn't the dielectric
"double-counted"? Instead of calculating a value related to
(q1*q2)/epsilon, it actually calculates (q1/epsilon)*(q2/epsilon), and thus
(q1*q2)/epsilon^2, correct? This effect wouldn't be noticeable for vacuum
calculations, but the difference is vital for dielectrics =\= 1. Can
anyone confirm this? Thanks.

Take care,
Samuel Bowerman
Ph.D. Candidate
Department of Physics
Illinois Institute of Technology
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Received on Wed May 27 2015 - 12:30:02 PDT
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