Desmond Tutorial

9 Analyzing Trajectories Using
VMD
Overview
Desmond provides extensions to VMD that facilitate trajectory analysis. VMD is primarily
a molecular visualization program, but it is a natural environment for analysis with its
strong support for atom selections, the ability to efficiently animate trajectories that contain
thousands of snapshots, and support for Tcl and Python scripting languages.
This section assumes a Unix/Linux environment and basic familiarity with VMD. If youʹre
just getting started with VMD, a number of excellent tutorials already exist and can be
found on the VMD home page:
http://www.ks.uiuc.edu/Research/vmd/current/docs.html#tutorials
The VMD Python Interface
The Python interface can be accessed from either the console (the terminal from which
you launched VMD), or from an Idle window that runs inside of VMD (preferred). To initiate
the Python interface in the console, simply type gopython at the vmd> prompt. To
launch the built‐in Idle window, youʹll need to set your PYTHONPATH properly as
described in the Desmond installation instructions.
The console command to launch the Idle window is
gopython -command "import vmdidle; vmdidle.start()"
You may wish to copy this command into your .vmdrc so that you open this window
every time you launch VMD. Once you have a Python prompt at either the console or the
Idle window, youʹre ready to start using the VMD Python interface.
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