Date: Sun, 18 Feb 2001 22:48:05 -0800 (PST)
From: Michael Crowley
Subject: Re: periodic box size

Regarding the box size, If you are using sander (not sander_classic)
the sizes will always be read from the bottom of the restart or
inpcrd regardless of what ntx says. You can override that
by specifying something other than ntx=7 and putting
a, b, and c inthe %ewald namelist. The only time the box info
from the prmtop file is used is when box information cannot be
found in the other two spots. So, the box information
from the restart is used ALWAYS, unless it is either not there,
or the user overrides it with ntx not 7 AND a, b, c are in the mdin.

Regarding fft dimensions, a good rule of thumb is to use
integers close to the box dimensions. Depending on what fft
library you are using, it is either a good idea or absolutley necessary that
you use integers that have prime factors 2, 3, and 5 and not any other
prime factors. FFT's generally run very slowly for other prome factors.
Thus, 43 is very bad, 40 or 45 would be better.

I hope that helps
Mike