VMD
Overview
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
Version 1.9.3 & 1.9.4 (alpha release) are available.
| Please do not run VMD directly on the login node. Such processes will be killed without warning. Instead, please use the srun command (see below). |
Restrictions on user access
VMD is not open source software. Please read the license before you request access. In particular please note:
- The software may be used for academic, research, and internal business purposes only.
- The software must not be used for commercial purposes. Commercial use includes (but is not limited to): (1) integration of all or part of the Software into a product for sale, lease or license by or on behalf of Licensee to third parties, or (2) distribution of the Software to third parties that need it to commercialize product sold or licensed by or on behalf of Licensee.
- Citation of the software must appear in any published work. See clause 6 of the above license and the VMD website for the required text.
- Export regulations including remote access: You must comply with all United States and United Kingdom export control laws and regulations controlling the export of the software, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. Please be aware that allowing remote access from outside the United Kingdom may constitute an export.
- Access to this software is not permitted for visitors or collaborators.
Requesting Access
To get access to VMD you need to be added to a unix group. Please email its-ri-team@manchester.ac.uk and confirm that you have read the above information and that your work will comply with the T&Cs.
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:
module load vmd/1.9.3-foss-2020a-python-2.7.18 module load vmd/1.9.4a57-foss-2022a (Python 3.10)
Further information about how to start X-Windows and GUI applications on the CSF (note this links to the CSF3 docs, the principles are the same, but make sure you put csf4 in the ssh command!).
We highly recommend using the Virtual Desktop Service when accessing this software on the CSF – it gives better compatibility with the CSF for this type of work than some desktops/laptops and it also offers a better compression of data across the campus network meaning it should run faster than it will if connecting directly from your own computer.
Running the application
Please use the interactive (srun) facility with –x11 flag to run VMD’s gui. The srun command itself is run on the login node, but it will then run VMD on a more powerful compute node – it tries to do this immediately, without needing a jobscript. For example:
# Run these commands directly on the login node (not in a jobscript). # The srun command will then run VMD on a more powerful compute node. module load vmd/1.9.3-foss-2020a-python-2.7.18 srun --x11 vmd
VMD will by default be restricted to a single CPU core.
Exiting the Application
Please quit VMD (via the GUI) when you have finished using it and this will cleanly terminate your interactive session.
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 srun / VMD:
export LIBGL_ALWAYS_INDIRECT=1
If that does not work try using the Virtual Desktop Service.
Further info
The VMD website has User Guides, Release Notes, and FAQs.
Updates
None.