I agree too, since hybridgb doesn't use the cap.
On Sat, Mar 27, 2010 at 12:36 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Agree ... let's deal with this in Amber12, at least for ipb /= 0 runs.
>
> All the best,
> Ray
>
> On Fri, Mar 26, 2010 at 7:21 PM, case <case.biomaps.rutgers.edu> wrote:
>
> > On Fri, Mar 26, 2010, Ben Roberts wrote:
> > >
> > > ifcap=1, hybridgb>0 = tested to an extent? I tried to read the manual
> > > here, and
> > > it didn't really explain the relationship between ifcap (as a setting
> in
> > the
> > > prmtop) and hybridgb. The manual suggests that what hybridgb is really
> > for, is
> > > the situation where waters beyond a certain distance away from the
> solute
> > (but
> > > determined by a number of waters to keep) are treated as a continuum.
> The
> > example
> > > (rem_hybrid) does not use ifcap.
> >
> > Sorry...my bad. I had assumed that hybridgb used ifcap. Since gb has
> never
> > been parameterized with waters, I'd suggest disallowing gb and ifcap
> > together.
> > Any other changes should to to Amber12.
> >
> > Comments welcome....dac
> >
> >
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> >
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Received on Sun Mar 28 2010 - 06:30:03 PDT
