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VMD

General
The VMD 1.8.6 program is available to users at NSC. VMD is a molecular builder and visualization program.

Program citation
The authors request that any published work or images created using VMD include the following reference: Humphrey, W., Dalke, A. and Schulten, K., ``VMD - Visual Molecular Dynamics'' J. Molec. Graphics 1996, 14.1, 33-38.

Manual
A manual is available. [here]

Essentials
VMD needs no input. Upon start the VMD interface consists of three windows: (i) the Control Panel, (ii) the View Window, and (iii) the Console Window. The program handles a large number of input and output file types; below we give a few examples but there are many others to explore.

Visualize Vasp input files (POSCAR)
In the Control Panel, choose "File ==> New Molecule". A new window opens in which you locate the Vasp input file, set the correct file type, and press "Load". The structure will appear in the View Window. You may change the atom display by, in the Control Panel, choosing "Graphics ==> Representations". A new window opens, in which you, under the tag "Draw style", can choose "Drawing Method" to be e.g. "CPK".

Visualize Vasp output files
Same as above but with choice of the "VASP_OUTCAR" file type.

Visualize repeated unit cells
You may change the number of illustrated unit cells by, in the Control Panel, choosing "Graphics ==> Representations". A new window opens, in which you, under the tag "Periodic", can add unit cells in the Cartesian directions by clicking in the respective boxes.

VMD on the visualization server Inspector
Start the program with the command

vmd
Note: Before accessing the files on the compute servers, you need to mount your home directories on these machines as secure shell file systems on Inspector [see details].




Page last modified: 2007-06-01 13:44
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