AMBER Archive (2007)

Subject: Re: AMBER: Electrostatic Energy in MD Simulation (GB)

From: David A. Case (case_at_scripps.edu)
Date: Thu May 10 2007 - 12:45:45 CDT

On Thu, May 10, 2007, adelene_at_stanford.edu wrote:
>
> When I run the "Coulomb" calculation in APBS, I do not get the same
> energy values as "elect.", which confuses me, because I expect them to
> be equal. They have similar trends (if I plot versus time), but
> "elect." is positive while that I calculated in APBS is negative.
>
> Does anyone have any insight?

My guess is that NAB and Amber are ignoring electrostatic interactions between
bonded atoms ("1-2" interactions) and between atoms bonded to a common atom
("1-3" interactions). APBS is probably giving you the total Coulombic energy.

...hope this helps....dac

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