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RMSDTT: RMSD Trajectory Tool


  • Jun 6 2014. Code is now available through GitHub. Version 4.0 now includes iterative fitting.


The RMSDTT plugin original goal was to add support for rmsd calculations and alignment of trajectories to the RMSD Tool plugin. It has since evolved to:

  • Calculate rmsd in trajectories, skip frames and do an all-to-all rmsd (all molecules/frames against each other).
  • Calculate weighted rmsd.
  • Align frames in trajectories.
  • Iterative fitting.
  • Plot results via the Multiplot VMD plugin (in all systems), Xmgrace (on unix systems) or MS Excel (on windows).
  • Save results to file.
  • Swap equivalent atoms (i.e. Glu OE1 and OE2) to reduce rmsd (if Swap plugin is available).
  • Generate basic statistics (average, standard deviation, minima and maxima).
  • Multi-line atoms selection with support for comments.
  • Highlight equivalent atoms of the rmsd selection.


The RMSDTT plugin is distributed as part of VMD (RMSDTT 3.0 since version 1.8.8, RMSDTT 2.0 since version 1.8.4).

The latest code is now accesible through its GitHub repository. Contact the author if you need an old version.


Documentation can be found in the GitHub repository.


Luis Gracia, PhD
Weill Cornell Medical College
1300 York Ave, New York, 10065 NY

Send comments and feedback to Luis Gracia.