AMBER Archive (2004)

Subject: AMBER: weird box expansion

From: Herbert Georg (hcgeorg_at_if.usp.br)
Date: Thu Jul 08 2004 - 11:57:57 CDT

Hi,

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

Herbert

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu