AMBER: weird box expansion

From: Herbert Georg <>
Date: Thu, 08 Jul 2004 13:57:57 -0300


I have performed simulations of a carbohydrate in water in a truncated
octahedron box in NPT ensemble and noticed that, despite the fact that the
program always displays a density of around 1 g/cm3, the box seems to be
expanded when viewed in vmd for example.
If I select water molecules around the solute up to a certain distance with
ptraj I see that the number of selected solvent molecules decreases
monotonically along with the trajectory.

Does anybody know what might be the problem?

Thanks in advance


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Received on Thu Jul 08 2004 - 18:53:00 PDT
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