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titleOverview

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

More information on VMD can be found here.

How to use 

To use VMD on NCI machine use the appropriate module 

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$ module load vmd/1.9.3

For more details on using modules see our software applications guide.

VMD is then invoked by typing 

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$ vmd

from an X-window console or a terminal console with X-tunneling.

Note

It may happen that your display window is not opening and throwing the following error. The error itself is an indication that OpenGL is not working well on your local computer. If you are using MobaXterm on Windows, go to Settings -> X11 and set OpenGL acceleration to hardware. MobaXterm restarted X11 server and now VMD should work.

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"MoTTY X11 proxy: unable to connect to forwarded X server: Network error: Software caused connection abort
ERROR) Tk startup error: couldn't connect to display "localhost:23.0"
X I/O error”

You may get the following error which causes not opening your display window. Enabling the indirect glx context in XQuartz of Mac OS by using either `defaults write org.xquartz.X11 enable_iglx -bool true` (for the new versions) or `defaults write org.macosforge.xquartz.X11 enable_iglx -bool true` (for the old versions) command, killing or restarting X server and then logging into Gadi with `-Y`option should solve the issue. Further information of enabling the indirect glx context is described at https://www.visitusers.org/index.php?title=Re-enabling_INdirect_GLX_on_your_X_server.

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XRequest.149: BadValue (integer parameter out of range for operation) 0x0
ERROR) Could not create OpenGL rendering context-> Exiting...
Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
Info) Unable to create OpenGL window.

The display window may not open and get the following error if you are using the indirect glx context enabled XQuartz installed on Mac OS with Apple M1 Pro chip (`glxinfo` shows OpenGL vendor string: Apple). In this case and other cases where your issue of opening the display window is not solved, we recommend to login to ARE (Australian Research Environment), start a Virtual Desktop instance, load vmd module and run vmd. Since the entire software stack (application + rendering) is in the same place and only the final rendered images are sent across the network in ARE, you will get better performance compared to the X-Forwarding.

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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 1.9.3 (November 30, 2016)
Info) Unable to create OpenGL window.

Licence requirements

To access VMD you need to have registered at the Developer's website and let us know your username. The user registration page is linked through the downloads so you will need to click an archive link (but you don't need to proceed to download as far as we're concerned). We are assuming that through the registration process you have read and agreed to the VMD licence agreement.

Once this is obtained, please request to join software group on https://my.nci.org.au if you wish to request access.

The registration process is the same as for NAMD so if you have already registered for NAMD you can provide those details.


Authors: Yue Sun, Andrey Bliznyuk, Mohsin Ali