VMD (Visual Molecular Dynamics)

Description

VMD (Visual Molecular Dynamics) is a molecular visualization program with 3-D graphics and built-in scripting for displaying, animating, and analyzing large biomolecular systems. It is also an effective front end visualisation and interaction package for simulations running on NAMD.

Licensing

UIUC Open Source Licence:
http://www.ks.uiuc.edu/Research/vmd/current/LICENSE.html

Users are required to agree to the terms and conditions of the licence before access can be granted. For further information contact us.

The authors require 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.

Application Homepage

http://www.ks.uiuc.edu/Research/vmd/

Basic Usage

VMD can be run as either an interactive or batch application.

Interactive Mode:
To run in interactive mode, first request an interactive session on one of the backend compute nodes via the scheduler. If compute facilities are available at the time of your request then a new terminal window will be launched.

qsh -cwd -V -l h_rt=01:00:00

will request an interactive shell with 1 hour of run-time (the -l h_rt parameter). Once in the interactive shell, enter these two commands to
start a graphical session:

module load vmd
vmd

After exiting VMD, enter the exit command in the interactive window to close the session.

Batch Mode:
As VMD has both a GUI and a text interface, scripts can be written to automate functions such as loading molecules, creating representations, making animations and analysing data. These commands can be entered in a batch script and then submitted through the batch queue in the normal way. An example script to create a movie of a molecular representation:

Further Resources

VMD tutorials:
http://www.ks.uiuc.edu/Research/vmd/current/docs.html#tutorials

Youtube:
https://www.youtube.com/watch?v=Fl3hmqCHYU4
http://www.youtube.com/watch?v=CJEZydlXQp4
http://www.youtube.com/watch?v=hChPzoEXK2Q