AMBER Archive (2005)

Subject: Re: AMBER: dynamics

From: David A. Case (case_at_scripps.edu)
Date: Sat Jan 08 2005 - 15:05:53 CST

On Sat, Jan 08, 2005, Germ?n Sciaini wrote:
>
> I am doing a dynamics of one iodide anion and 216 ammonia molecules. I am
> using the keyword setBox ----- vdw to create the box. I would like to know
> if the dynamics could carry out any problem when the iodide is at the edges
> of the box (for instant, problems in the iodide?s solvation shell).
> Is it better use the keyword solvateBox in order to put the iodide in the
> box?s center?
>

setBox and solvateBox to very different things.

setBox just sets up the box parameters (lengths of the sides and angles); all
of the ammonia molecules already have to be there, and in the right place.

solvateBox would *add* ammonia molecules around your iodide ion, and in
addition set up the proper box parameters. So, here you would just start with
a iodide ion, whose absolute coordinates are irrelevant.

It is generally easiest to use solvateBox, but not always. If you already
have a good set of ammonia + iodide coords, you use setBox. Be sure to check
carefully that you are getting what you want.

..good luck...dac

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