To follow up my own question
Solution: use netcdf format
It looks like VMD doesn't read the pbc dimensions or angles (or something)
correctly (as is in version 1.8.7) when coordinates are in "amber7
coordinate" format, but it does read the pbc information correctly and
displays the periodic images correctly (without the diamond shaped holes)
when the coordinates are in the net cdf format.
-----Original Message-----
From: Paul Brandt [mailto:brandt.j.gene.com]
Sent: Monday, June 21, 2010 2:54 PM
To: 'AMBER Mailing List'
Subject: Re: [AMBER] periodic images of truc. octahedron in vmd
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?
Thanks!
Paul
-----Original Message-----
From: Bill Ross [mailto:ross.cgl.ucsf.EDU]
Sent: Monday, June 21, 2010 2:11 PM
To: amber.ambermd.org
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.
Bill
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Received on Mon Jun 21 2010 - 16:30:03 PDT
