VMD plugins at WMC Physiology & Biophysics

iTrajComp: interactive Trajectory Comparison

(former RMSDTT2)

Preview

The iTrajComp plugin is a general analysis tool for trajectories. It is under heavy development, but it can already do a few interesting things (no guarantees, though!). In hopes of helping our fellow VMD users, this webpage will host the preview releases of the tool. If you are interested in trying this tool, please contact Luis. Once we are confident that the plugin is doing what it should and we get some time to write a little manual, it will be freely available from this webpage.

Note: This plugin is the former RMSDTT2 plugin. We decided to change the name a) to avoid confusion with the RMSDTT plugin, and b) because it is designed to do much more than simple calcuating the rmsd.

Now, briefly, the features of the plugin:

• Data calculations:
  • RMSD:
    • coordinates (traj(1) vs [traj(1) or traj(2)])
    • labels (distance, angles, dihedrals)
  • Number of:
    • contacts within a cutoff
    • hydrogen bonds within a cutoff, angle (as defined in VMD)
• Objects:
  • matrix representation
  • interaction with VMD main window (structures involved in the data clicked will be represented in VMD)
  • multiple simultaneous objects
  • combination of objects in a new object
  • save the data in 4 file formats

A few preview images: