VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 13 2006 - 13:55:15 CDT

Rob,
  At present, if you load only a volumetric dataset into a molecule,
there isn't a way to set it's periodicity. The current implementation
demands that you have some atomic coordinates loaded in the molecule before
you can use the periodic display feature. If you load both an atomic
structure (even a 1 atom placeholder) and a volumetric dataset, you will
be able to set the a/b/c/alpha/beta/gamma periodic boundary information.

While this may appear odd to you initially, the reason why VMD doesn't
already provide a means of doing this is because none of the volumetric map
file formats currently supported by VMD include information about periodicity.
They do include the volumetric cell dimensions of course, but not all such
datasets are periodic, and in many cases the volumetric cell dimensions do
not match the periodic cells for atomic datasets, which is why the volumetric
cell dimensions don't simply override the atomic data of this type.

One thing that I could easily change in VMD would be to modify the periodic
display feature so that in the case when ONLY a volumetric dataset is loaded
into a molecule, the periodic cell information will be taken from the
volumetric dataset. Another method might be to add a selector that lets
you choose between per-timestep PBC info, and the volumetric cell data for
one of the other datasets. That might be more flexible and less apt to
surprise a new user.

In the mean time, you can workaround the existing limitation by loading a
one-atom PDB file with your volumetric data, and set the periodic cell
information in the PDB CRYST1 record if you like. That will allow you to
use the PBC display feature with your purely-volumetric VASP data for the
time being.

Let me know if you need help with this.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Oct 12, 2006 at 09:24:26PM -0700, Rob wrote:
>
> Hi all,
>
> I use VMD exclusively with the VASP interface, but
> I think my question applies to general shortcomings
> of VMD. I'm currently using VMD 1.8.5.
>
> When I load simply the coordinates of a set of atoms
> in a unit cell, I can see the periodic replications
> by checking the Periodic checkboxes in the window
> of the "Graphical Representations".
>
> However, when I load volumetric data (e.g. in VASP
> this is the charge density), the periodic checkboxes
> are there but they don't work at all. Is this a bug?
>
> I really would like to extend this volumetric data
> according to the periodic boundary conditions, so
> that I can replicate both the atoms and the
> corresponding volumetric data.
>
> Regards,
> Rob.
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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