Re: amber-developers: leap counterions and solvate refs

From: Volodymyr Babin <>
Date: Fri, 21 Nov 2008 10:29:40 -0500 (EST)

Hi Scott,

I have no idea about the references; I believe that
solvateBox/solvateOct use pre-equilibrated box of solvent,
copy it as many times as needed and then discard unwanted
(too close/far to/from the solute) solvent molecules;
addIons tries to place the ions in the places with maximum/minimum
electrostatic potential (it does not really do that; it does
not take periodicity into account either). I would answer
the reviewer question as follows: "the recipes used to place
the counterions and waters are irrelevant because before the
data gathering stage the water and the ions were allowed to
reach thermal equilibrium and therefore have forgotten (presumably)
their initial positions; to check this point we verified our
calculations by performing several runs using different random
generator seeds/random velocities/etc".

Have a great day,

On Thu, November 20, 2008 21:47, Scott Brozell wrote:
> Hi,
> A reviewer has asked for details on how leap places counterions and
> waters.
> I'm looking for literature references ?
> I didn't find any in the manual, source code, or
> Case, et al. Journal of Computational Chemistry Volume 26, p1668 (2005).
> And my limited library access does not provide
> Pearlman, et al. Comp Phys Commun 1995, 91, 1.o
> thanks,
> Scott
Received on Fri Dec 05 2008 - 16:15:50 PST
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