VMD

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

Available

• Puhti: 1.9.3
• Mahti: 1.9.3

License

• The use of the software is restricted to non-commercial research, see detailed license description.

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 to use it through the Puhti web interface remote desktop. Please don't run VMD on the login nodes.

Note

For improved 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

• VMD home page
• VMD Tutorials
• VMD Manuals

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