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 - 09:00:04 PDT
