| The CSF2 has been replaced by the CSF3 - please use that system! This documentation may be out of date. Please read the CSF3 documentation instead. To display this old CSF2 page click here. |
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 1.8.7 and 1.9 are available. These are binary installs (i.e. no compilation involved).
| Please do not run VMD directly on the login node. Such processes will be killed without warning. |
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
You will need to connect to the CSF using ssh -X to have the display exported to your local machine. You should then load the appropriate VMD module using the module command to access the executables:
- For VMD 1.8.7:
module load apps/binapps/vmd/1.8.7 - For VMD 1.9:
module load apps/binapps/vmd/1.9
Further information about how to start X-Windows and GUI applications on the CSF.
Running the application
The application is launched by issuing the command vmd.
If you need to run the software for more than a few minutes using significant CPU or memory resources you should run it via a compute node thus:
qrsh -V -l inter -l short vmd # # If you get an error about OpenGL see below
VMD will by default be restricted to a single CPU core. If you wish to run VMD multicore then you must override a VMD environment variable as follows:
# Using 4 cores for example export VMDFORCECPUCOUNT=4 qrsh -V -l inter -l short -pe smp.pe $VMDFORCECPUCOUNT vmd # # If you get an error about OpenGL see below
Exiting the Application
Please quit VMD (via the GUI) before you exit your ssh/PuTTY login session on the CSF. If you simply quit your ssh application (e.g., kill PuTTY in Windows) then VMD is left running on the CSF.
Hints, Tips, Fixes
Fix for OpenGL Error
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 qrsh / VMD:
export LIBGL_ALWAYS_INDIRECT=1
Nvidia GPUs
VMD will make use of Nvidia CUDA hardware if present. This will accelerate raytraced rendering and implicit ligand sampling. If you have access to the GPU hardware (see GPUs on the CSF) you can run VMD as follows:
unset VMDFORCECPUCOUNT qrsh -V -l inter -l nvidia vmd
Please also consult the qrsh documentation for more detailed instructions.
Further info
The VMD website has User Guides, Release Notes, and FAQs.
Updates
May – 2013 – Updated docs re OpenGL error fix
March 2013 – Updated docs re multicore and GPUs.
April 2011 – Version 1.9 installed.
March 2011 – Version 1.8.7 installed.