On Wed, Feb 20, 2013 at 6:50 PM, Mo Chen <mc842.cornell.edu> wrote:
> Dear Amber users/developers,
>
> I have a question about the definition of EPTOT in Amber. Does it
> include the part of potential energy that comes from interaction
> between atoms at the edge of the primary box and that in the images
> (i.e. the imaging atoms that are within cutoff of the primary box
> atoms)?
>
Yes it does. Amber uses the "minimum image convention". You can think
about this as meaning that every particle 'feels' like it is at the center
of the periodic cell.
In periodic simulations, EPTOT represents the _full_ potential energy of
_every_ particle in one periodic cell interacting with every other particle
in every periodic cell (in Amber, only the electrostatic terms are
calculated past the length of a single unit cell).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Feb 20 2013 - 17:00:02 PST
