On Thu, Feb 25, 2016, Ross Walker wrote:
>
> I never really understood the purpose of noshakemask since you have
> to run with a 1fs timestep if you use it so you might as well shake
> nothing at all. Except if you still want to use a triangulated water
> model rather than a flexible water model. But even then one would sure
> just want shake on the waters and everything else unshaken no?
No: one also needs shake with hydroxyls (Ser, Thr, Tyr, etc.) which have zero
vdW radii on the protons. One can often "get away" with not shaking these,
but only if you a lucky and don't run for all that long.
> > (Actually, there's something more subtle here because the offset
> > seems to apply to the X-H bonds, in particular, and not the heavy-atom
> > bonds, but I haven't been able to perform a complete pathology)
With ntc=2, Amber only shakes bonds to hydrogens. Generally, that is all that
anyone really uses, since shaking heavy atom bonds is not supported for
parallel runs, or for qmmm.
....dac
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Received on Fri Feb 26 2016 - 10:30:03 PST
