Re: [AMBER] Bug in LIE action command of cpptraj?

From: Jason Swails <>
Date: Wed, 27 May 2015 15:34:20 -0400

On Wed, May 27, 2015 at 3:25 PM, Samuel Bowerman <> wrote:

> 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?

​Yes, you're right. The charges should be divided by the square root of
the dielectric for precisely this reason. My mistake.

I probably shouldn't have added the "diel" keyword at all, though. LIE is
inherently an explicit solvent method, so I wouldn't recommend the use of a
non-unity dielectric.

​Thanks for the report,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed May 27 2015 - 13:00:02 PDT
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