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Warning!

Puhti and Mahti are being decommissioned in stages, and their storage areas will become fully unavailable from 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.

Puhti scratch is very full: keep only active data there and move or delete everything else. No new Puhti scratch quota will be granted.

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

  • Puhti: 1.9.3
  • Mahti: 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 HPC web interface remote desktops. Please don't run VMD on the login nodes.

Running VMD with GPU-accelerated graphics on Puhti

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

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