On Wed, May 27, 2015 at 3:25 PM, Samuel Bowerman <
sbowerma+amber-l.hawk.iit.edu> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 27 2015 - 13:00:02 PDT
