AMBER Archive (2004)

Subject: Re: AMBER: weird box expansion

From: Herbert Georg (hcgeorg_at_if.usp.br)
Date: Thu Jul 08 2004 - 12:38:01 CDT

Well then if I'm not interested in calculating diffusion constants, there should
be no reason to use IWRAP=0, am I right?

Thomas E. Cheatham, III escreveu:
>>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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