Re: [AMBER] box size changing during equilibration

From: Daniel Roe <>
Date: Wed, 19 Nov 2014 08:26:45 -0700


Normally when you build a system with any kind of solvent the starting
density isn't quite right, so during your initial equilibration with
constant pressure the box size will adjust so as to relax the density
of the system. In fact, until your density equilibrates you should
continue to run with constant pressure; otherwise you run the risk of
developing vacuum bubbles in your solvent (if your density is too
low). Once your density has equilibrated you can switch to constant
volume to keep the box size fixed.


On Wed, Nov 19, 2014 at 8:20 AM, Robin Jain <> wrote:
> Dear sir,
> I have simulated my system and i used a cubic box with cell size 17.58 A
> but on equilibrating the system the cell size become 18.05 A. What happens
> behind that and what can i do for keeping the box size constant.
> --
> Robin Jain
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Nov 19 2014 - 07:30:03 PST
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