Re: AMBER: too much vacuum in the box created by Leap

From: Carlos Simmerling <>
Date: Fri, 11 Feb 2005 08:21:23 -0500

that's expected. there is really no way to get water perfectly around
the solute
or box edges, because you are carving a hole and need to take away things
that overlap even sloghtly, leaving space. it's been discussed on the email
list many times, check the archive.

your box is very anisotropic- I hope that you're restraining your solute
since you will have some serious problems if it rotates (which it should).

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:

Marie-Pierre Durrieu wrote:

> Dear all,
> I still have problems with the box created by Leap. It seems that the
> box of water contains too much vacuum. I wanted a rectangular box with
> a minimimum distance between the solute and the wall of the box of
> 18A. During my heating procedure in (N,V,T) ensemble, the molecules of
> water rearrange so that the system forms a new rectangle inside the
> box, with huge layers of vacuum (
> Then when I turn on constant pressure for equilibration the box
> reduces and finally matches the system, but along the axe x the box
> dimensions have been reduced by 10A, so the box is much smaller than
> the one I wanted. Of course I expected that the box would reduce when
> switching from constant volume to constant pressure, but not that much.
> Did anyone experience the same problem with the box created by Leap ?
> Leap seems to add small boxes of water perhaps badly equilibrated,
> which leads to too much vacuum that gives strange things during a MD
> simulation with constant volume.
> Thanks in advance,
> Marie-Pierre.
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Received on Fri Feb 11 2005 - 13:53:00 PST
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