From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Sep 26 2013 - 00:56:36 CDT

On Thu, Sep 26, 2013 at 3:14 AM, Jaap Kroes <jaap.kroes_at_epfl.ch> wrote:
> Dear VMD developers,
>
> Likely you are already aware, but I believe there is a problem with
> non-orthorhombic cells in VMD.
> Upon looking trough the mailing list I only found some old topics,
> where this problem already seemed to be present.
> Is this still the case?
>
> The example at the end of this mail works fine in xcrysden but not in VMD.

which version of VMD? have you tried the latest alpha test binary?
there was an issue with the rotation of cell vectors (and coordinates)
to comply with the requirements in VMD for correct PBC display. this
was fixed in april.

axel.

> When manually specifying the unit vectors with the 'pbc' module
> pbc set {4.26000000 0.00000000 0.00000000 0.00000000
> 2.13000000 1.22975607 0.00000000 -3.30000000 5.71576766}
> -namd
> I get the error "vecdot needs vectors of the same size: 1.0 : 1 0 0".
>
> Thanks!
>
> Best,
> Jaap
>
> Below is a rotated graphite xsf-file, which loads fine in xcrysden
> ('graphite.xsf')
>
> CRYSTAL
>
> PRIMVEC
> 4.26000000 0.00000000 0.00000000
> 0.00000000 2.13000000 1.22975607
> 0.00000000 -3.30000000 5.71576766
>
> PRIMCOORD
> 8 1
> 6 0.00000000 0.00000000 0.00000000
> 6 1.42000000 0.00000000 0.00000000
> 6 1.42000000 -1.65000000 2.85788383
> 6 2.84000000 -1.65000000 2.85788383
> 6 2.13000000 1.06500000 0.61487803
> 6 3.55000000 1.06500000 0.61487803
> 6 3.55000000 -0.58500000 3.47276187
> 6 4.97000000 -0.58500000 3.47276187

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.