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 is available. This is a binary install (i.e. no compilation involved).

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.

A copy of the license is also available on the CSF in: /opt/apps/apps/binapps/vmd/vmd-license-accessed-13dec2018.pdf

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 apps/binapps/vmd/1.9.3

Further information about how to start X-Windows and GUI applications on the CSF.

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 (qrsh) facility to run VMD. The qrsh 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 qrsh command will then run VMD on a more powerful compute node.

module load apps/binapps/vmd/1.9.3
qrsh -cwd -V -l short vmd 

(that’s an UPPERcase V)

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
module load apps/binapps/vmd/1.9.3
export VMDFORCECPUCOUNT=4
qrsh -cwd -V -l short -pe smp.pe $VMDFORCECPUCOUNT vmd

Exiting the Application

Please quit VMD (via the GUI) before you exit your qrsh session on the CSF. If you simply quit your connection to the CSF then VMD may be left running on the CSF and consuming resources unnecessarily.

Hints, Tips, Fixes

Black Window Fix for XQuartz on MacOS

On MacOS, some users have reported that the VMD runs and displays most of the GUI, but the main render window, where the molecule is displayed, remains completely black.

Please try the following if you have the black-window issue:

# On your Mac, in a terminal that is NOT logged in to the CSF:
defaults write org.xquartz.X11 enable_iglx -bool true

# Now login to the CSF using:
ssh -Y username@csf3.itservices.manchester.ac.uk

# Then run VMD as detailed earlier, EG:
module load apps/binapps/vmd/1.9.3
qrsh -cwd -V -l short vmd

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

If that does not work try using the Virtual Desktop Service.

unset VMDFORCECPUCOUNT
qrsh -V -l inter -l nvidia vmd

Please also consult the qrsh documentation for more detailed instructions.

Using Plugins e.g. PLUMED

If you would like to use a plugin, such as PLUMED. You should load the module apps/intel-17.0/plumed/2.4.0 before the vmd one, then you will be able to use the analysis at: Extensions > Analysis > Collective variable analysis (PLUMED)

External Plugins

The following external / 3rd-party plugins have been installed. You’ll find them in the Extensions menu, in one of the categories off that menu – e.g., Analysis). New plugins appear at the bottom of each menu:

• Density Profile Tool (Analysis menu) – See https://data.mendeley.com/datasets/9n2kdsf2t9/1

Further info

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

Updates

None.