AMBER Archive (2006)

Subject: Re: AMBER: iso command and a cubic box

From: David A. Case (
Date: Wed Jul 12 2006 - 14:00:25 CDT

On Wed, Jul 12, 2006, Patricia Hunt wrote:
> I'm trying to understand AMBER 9.0 solvate box command, I want a
> perfectly cubic box, however the iso command in solvate box doesn't
> seem to be giving me that.

> 27.1882150 27.1884770 27.3464510 90.0000000 90.0000000 90.0000000
> Which is not cubic. How can I enforce a cubic box?
> Is it safe to just manually change these dimensions? Will it muck
> other things up?

I don't know quite why you don't get the perfect cube, but you should be able
to manually modify the bottom of the inpcrd file to make all three values the
same. When you run constant pressure equilibration set ntp=1 and the cube
*should* stay as a cube (at least as I read the code.)

...good luck....dac

(p.s. I know I still owe you info about octahedral molecules!)
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