VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon May 22 2006 - 23:25:18 CDT

On Mon, 22 May 2006, Berit Hinnemann wrote:

BH> Hi all,

berit,

BH> I would like to simulate charge density differences calculated with VASP
BH> (CHG file) with VMD and I therefore need to write a function that converts
BH> the VASP format to Gaussian Cube (if anybody has done this already, I would

alternatively you could write a script, that will read the file and add
it directly to VMD as a volumetric data set (or create a hacked clone of
the cube plugin to support the file format natively). see:
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/readcube/
http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/cubeplugin.html
the second URL also contains a description of the format.

BH> be grateful for any hints on this). Can vmd handle non-orthogonal unit cells
BH> (I have a hexagonal unit cell)? Where in the vmd pages can I find a

non-orthogonal cells work. however on loading the cell and its
embedded coordinates have to be rotated to accomodate the
PBC conventions currently employed by VMD. see the cubeplugin docs.

BH> description on how exactly the cube file should look like? I have looked
BH> around on the vmd website but I am unsure about several things, e.g.
BH> cartesian/atomic units and requirements on the orientation of the unit cell.

see the cubeplugin docs. cube files are _always_ in atomic units.

please let us know, if you need additional help.

best regards,
    axel.

BH>
BH> Any hints would be greatly appreciated. Thanks, Berit
BH>
BH>
BH>
BH> Berit Hinnemann, Ph.D.
BH> Princeton University
BH> Department of Mechanical and Aerospace Engineering
BH> D310 Engineering Quadrangle
BH> Princeton, NJ 08544
BH> email: bhinnema_at_princeton.edu
BH> tel: (609)-258-2651
BH> fax: (609)-258-5877
BH>
BH>
BH>
BH> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.