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

From: Samuel Bowerman <>
Date: Wed, 27 May 2015 15:07:21 -0500

Hi Jason,

Thanks for the response. Perhaps you could enlighten me as to what part of
the calculation is inherently explicit? For example, if I want to analyze
the specific interaction of a ligand with a small subsection of the binding
protein, I define two groups: "ligand" and "subset (surroundings)". How
does explicit vs implicit matter for this case if I am only calculating
pair-wise point-charge energies for these groups? If I were to define only
the ligand group, then the surroundings would include the explicit waters,
but that may not always be the case, correct? Or am I not thinking about
this correctly?


On Wed, May 27, 2015 at 2:34 PM, Jason Swails <>

> 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
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed May 27 2015 - 13:30:02 PDT
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