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
- 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 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.