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Visual Molecular Dynamics (VMD)

Overview

VMD, or Visual Molecular Dynamics, is a modeling program that allows you to visualize and interact with molecular systems in 3D. This program pairs well with NAMD, which can be used to simulate and analyze large structures over time. Due to its use of a GUI, you'll want to either use Desktop Mode in OnDemand or X11.

Availability

Cluster Module/Version
BOSE vmd/1.9.3
vmd/1.9.4
BGSC Not Available

Note: You can simply use "module load vmd" to activate the most recently installed version of this software.

How To Access

Access to VMD is best done by using Desktop Mode in our web-based Open OnDemand platform, which lets you access our computing infrastructure using your web brower.

You can also use X11 over SSH, however that is not recommended as it is less performant and more complicated and as such is not currently covered in this guide.

Desktop Mode

  1. Log into Open OnDemand - https://ondemand.hpc.uwec.edu
  2. Click "Desktop" on the dashboard, or by first clicking "Interactive Apps" in the top bar.
  3. Fill out your required resources to the best of your abilities. Unsure what to use?
  4. Wait for the job to start, then click "Launch Desktop"
  5. Start the terminal by clicking on the black square icon in the top bar, or by going to Applications --> System Tools --> MATE Terminal"
  6. Type: module load vmd
  7. Type: vmd

VMD Example

Real Example

Has your research group used VMD in a project? Contact the HPC Team and we'd be glad to feature your work.

Citation

Please include the following citation in your papers to support continued development of VMD.

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

Resources