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

From: Paul Brandt <>
Date: Mon, 21 Jun 2010 14:54:09 -0700

Thanks for the reply.

The system is fully equilibrated, the simulation is NPT. With iwrap turned
on, the voids do not fill in. I think that VMD is just not aware of the
periodicity of the truncated octahedron.

Is there a way that anyone knows of to correct this or another viewer that
will display the periodicity of such simulation cells correctly?


-----Original Message-----
From: Bill Ross [mailto:ross.cgl.ucsf.EDU]
Sent: Monday, June 21, 2010 2:11 PM
Subject: Re: [AMBER] periodic images of truc. octahedron in vmd

> 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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