Thanks all,
I must confess, I have detailed knowledge of how LAMMPS has coded shake,
but not AMBER. Is there a formula someone could point me towards, or a code
line number, where I could see the energy with shake present? This is no
way would influence the dynamics, however, correct?
Regards,
Conor Parks
B.S.E in Chemical Engineering, University of Michigan, 2012
PhD candidate in Chemical Engineering, Purdue University
On Thu, Oct 15, 2015 at 10:56 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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 - 08:30:03 PDT
