physiology

VMD plugins at WMC Physiology & Biophysics

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.

Within this page you will find VMD plugins developed in our group. Other plugins can be found at the main VMD plugin library.

These plugins were developed totally or partially at the department of Physiology and Biophysics at Weill Cornell Medical College.

Many people seem to have problems installing these plugins. To help with this issue I have written a small guide on how to install third party VMD plugins in a central location without modifying the VMD installation.

Available plugins are:

3.0 (5 Aug '10)

RMSDTT: RMSD Trajectory Tool

Tool for rmsd calculation and alignment of trajectories.
Preview (4 Apr'06)

iTrajComp: iterative Trajectory Comparision

A graphical and interactive tool for analysis and comparison of trajectories: rmsd, contacts, hbonds, labels, ....
1.0 (4 Apr'06)

Swap: swapping coordinates between atoms

Provides functions to swap coordinates between atoms in a molecule. Aimed primarily at reducing rmsd calculations can be used within the RMSDTT plugin, but uses are up to the user imagination.
2.0 (7 May'12)

Clustering

Clustering is a VMD plugin to visualize clusters of conformations for a trajectory. Imports output from popular clustering programs.