VMD (Visual Molecular Dynamics) - Interactive Molecular Visualization and Analysis Software


VMD is a powerful molecular dynamics visualization and data analysis program which is designed for displaying and animating large biomolecular systems and performing data analysis on such data sets.

Running VMD on Spear

In order to run VMD on the Spear system, first log into spear using your HPC login credentials with either SSH with X11 forwarding or XPRA. Then simply call VMD from the command line by typing the following command:


This will launch the GUI for VMD. From here, you will be able to load the molecular data set that you want to work with through the main GUI command window. Further documentation as well as tutorials can be found here under the "Documentation and Support" section.

Running VMD on HPC

Running VMD on the HPC Login nodes is possible as well. First log in to one of the HPC Login nodes using SSH with X11 Forwarding using the -Y option. Then simply call VMD from the command line just as above and the program will launch the GUI for VMD.