Thank you! That cleared up the issue for me! My brain read constraint
instead of restraint :)
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 11:58 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, Oct 15, 2015 at 11:15 AM, conor parks <coparks2012.gmail.com>
> wrote:
>
> > 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?
> >
>
> ​SHAKE are constraints, not restraints, and as such should not affect the
> energy. As long as the SHAKE tolerance is high enough (which it is by
> default), the bonds never deviate from ideality enough to make a meaningful
> contribution to the bond energy (and users usually set ntc=2 to omit those
> bonds from the energy term, anyway).
>
> Again, we were talking about Cartesian and collective variable
> *restraints*, which have an energy term like E=k*(x-xeq)^2 (which obviously
> impacts the potential energy, since it adds a "restraint" term to it).
> SHAKE was not part of the discussion.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Oct 15 2015 - 10:30:04 PDT
