VMD-L Mailing List

From: Jaap Kroes (jaap.kroes_at_epfl.ch)
Date: Wed Sep 25 2013 - 20:14:39 CDT

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.
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