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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

VMD

VMD (Visual Molecular Dynamics) is a molecular visualization program for displaying, animating, and analyzing large (bio)molecular systems using 3D graphics and built-in scripting.

Available

  • Roihu-CPU: 1.9.3

License

Usage

Initialize with:

module load vmd/1.9.3

Note, that you need remote graphics to work with VMD. Due to the heavy graphics required by VMD, we recommend using it through the Roihu web interface remote desktop. Please don't run VMD on the login nodes.

Running VMD with GPU-accelerated graphics on Roihu

For even better performance, you can run VMD with GPU acceleration in the Roihu web interface. In this case, select Accelerated Visualization instead of the plain Desktop app.

It is in principle also possible to run VMD over X11. In this case, see the instructions on starting an interactive application with X11 graphics. However, using X11 to run VMD is very slow and thus discouraged.

References

The authors request that all published work which utilizes VMD include the primary VMD citation at a minimum:

Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.

Consult "How to cite VMD" for further details.

More information