AMBER Archive (2004)

Subject: Re: AMBER: weird box expansion

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Thu Jul 08 2004 - 12:06:57 CDT

> 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.

Likely IWRAP=0 so imaging is not occuring. Search the archives (imaging,
iwrap) at

        http://amber.ch.ic.ac.uk/archive/

for a more verbose answer, but likely simply the water is diffusing to
adjacent periodic cells.

You can try using ptraj to image

  trajin mdcrd
  trajout mdcrd.imaged
  center mass origin :1
  image origin center familiar

If IWRAP=1, then this is a more severe problem and more details will be
necessary to decipher.

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