VMD

Overview

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Versions 1.8.6, 1.8.7, 1.9 and 1.9.1 are available. These are binary installs (i.e. no compilation involved).

Restrictions on user access

There are no restrictions on accessing VMD, but all users should read and observe the license. In particular it should be noted that:

• VMD is for academic, research and internal business purposes only, e.g. not for commercial use. A definition of commercial use is given in clause 7.
• Citation of the software must appear in any published work. See clause 6 and the VMD website for the required text.

A copy of the license is also available on the CSF in: $VMD_HOME/vmd/LICENSE .

Set up procedure

It is recommended you use the nyx3 virtual desktop from which to access the iCSF GPU node. Please see the instructions on vglconnect for how to log in to the iCSF GPU node.

On the iCSF GPU node you should then load the appropriate VMD module using the module command to access the executables:

• For VMD 1.9.1: module load apps/binapps/vmd/1.9.1
• For VMD 1.9: module load apps/binapps/vmd/1.9
• For VMD 1.8.7: module load apps/binapps/vmd/1.8.7
• For VMD 1.8.6: module load apps/binapps/vmd/1.8.6

Running the application

The application is launched by issuing the command vmd.

If running on jabberwock, the iCSF GPU node, having connected to jabberwock using vglconnect then run VMD via vglrun using

vglrun vmd

VMD will by default be restricted to a single CPU core. Most of the time this should be sufficient. If you wish to run VMD multicore then you must override a VMD environment variable as follows:

export VMDFORCECPUCOUNT=4

where the number is how many cores you require.

Fix for OpenGL Error

You should not need to do this if using vglrun to run VMD.

You may get an error message from VMD about OpenGL such as:

ERROR) A TrueColor visual is required, but not available.
ERROR) The X server is not capable of displaying double-buffered,
ERROR) RGB images with a Z buffer.   Exiting ...
Info) VMD for LINUXAMD64, version 1.9 (March 14, 2011)
Info) Unable to create OpenGL window.

Try setting the following variable before running VMD:

export LIBGL_ALWAYS_INDIRECT=1

Further info

The VMD website has User Guides, Release Notes, and FAQs.

Updates

None.