I believe the ethanol parameters may also be responsible for the sloshing...
I had really tried to incorporate gravity into ff14SB, but couldn't figure
out if the 1-4 interactions should be scaled or not. So I consulted the
same statistical tool I use for every scientific decision: a single toss of
a fair coin. The results of this gravitational experiment convinced me that
gravity did not think it was needed. In hindsight, failing to solve this
problem was a key limitation. Thank you for finding such an apt solution
and really bringing AMBER force fields to the next level!
On Wed, Apr 1, 2015 at 10:36 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> Dan,
> Turn off imaging in the dish model, that will help with spills. The fast
> translation causes sloshing.
> Carlos
> On Apr 1, 2015 10:10 AM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
>
> > On Wed, Apr 1, 2015 at 5:12 AM, Jason Swails <jason.swails.gmail.com>
> > wrote:
> > > The Particle-Mesh-Ewald method has been modified to support the
> > functional
> > > form of gravity, so that the full range of the gravitational
> interaction
> > > between particles in an infinitely periodic system is fully accounted
> > for.
> > > We are optimistic that this work will be available for the upcoming
> > > AmberTools 15 release, released as leaprc.ff14SBgrav.
> >
> > This is great news and fixes one of the issues that had been keeping
> > me from completing my "dish" water model. The only thing I need to
> > figure out now is out to prevent the water from spilling during my
> > simulations. Thanks Jason!
> >
> > -Dan
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Apr 01 2015 - 08:00:05 PDT
