AMBER: too much vacuum in the box created by Leap

From: Marie-Pierre Durrieu <>
Date: Fri, 11 Feb 2005 13:53:35 +0100

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 Durrieu
Institut de Biologie Physico-Chimique
13 rue Pierre et Marie Curie
75 005 Paris - FRANCE
e-mail :
Tel: +33 15841 5161
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Received on Fri Feb 11 2005 - 13:53:00 PST
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