Re: [AMBER] periodic images of truc. octahedron in vmd

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Mon, 21 Jun 2010 14:10:37 -0700

> Does anyone know, does VMD correctly display the periodic images of a
> truncated octahedral simulation cell created with leap? I see empty space
> in between the cells. This isn't right is it?

If the system is not equilibrated, one would expect to see a gap
between cells because of the way waters are placed initially.
This is why one needs constant pressure equilibration, to shrink
the box and lose vdw voids.


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Received on Mon Jun 21 2010 - 14:30:04 PDT
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