AMBER Archive (2003)

Subject: Re: AMBER: solvatebox-solvateshell

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Sat Sep 06 2003 - 15:16:38 CDT

> I prefer to use solvateshell instead of solvatebox to
> decrease the time, but I am not sure if it is really
> better and I don't know what I should do for periodic
> boundary conditions. I would appreciate if someone
> helps me.

Although the spherical shell may be a little faster (due to lack of a need
to calculate a reciprocal sum as required in the Ewald calculations), and
further it avoids potential artifacts from periodic images, the spherical
shell overall is not fully recommended since (a) you would likely need to
run a longer cutoff for stability (something like 12 angstroms), (b) you
have a vacuum-solvent interface that will perturb the water structure, and
(c) the solute may drift outside the solvent shell (unless cap forces are
applied which will exacerbate the already large pressures created by the
solvent blob).

If you do some timings comparing a solvent blob (with a 12 angstrom
cutoff) to a PME simulation in a truncated octahedral box (with a 9
angstrom cutoff), likely the difference in simulation time will not be so
great.

A truncated octahedron, created with solvateOct in LEaP, is like a cube
with the corners cutoff. It is not too far from a sphere in its size.
If you are covering your *entire* solute with the solvent blob, a
truncated octahedron (with a solvateOct and a 9-11 angstrom buffer) is a
reasonable choice. You still have to worry about potential artifacts from
periodicity, however this is less severe than the solvent-vacuum interface
artifacts. If you are only covering part of your system with solvent and
a solvent sphere, then you may get a speed-up, but suffer consequences
from the solvent-vacuum interface. In this case, stochastic boundary
simulations may be better however this is not implemented in AMBER at
present...

Good luck,

\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, Depts of
| Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry
| Adjunct Asst Prof of Bioengineering; Center for High Performance Computing
| University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT 84112
|
| tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418 http://www.chpc.utah.edu/~cheatham

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