On Thu, Oct 15, 2015 at 10:17 AM, Conor Parks <coparks2012.gmail.com> wrote:
> Now I am curious, Dac. Why would the answer change if restraints are
> present? Are you referring to constraints as in settle or shake? In my
> view, these should not change the energy.
>
And sometimes you will also see a term "EAMBER" which is the total
potential energy *without* counting the restraints. Obviously you don't
want to add this value when trying to compute EPtot from the printed
components, because then you'll double-count everything except the
restraint energies :).
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 15 2015 - 08:00:05 PDT
