Changes between Version 3 and Version 4 of Scripts/MMTK

Timestamp:

Sep 3, 2010, 1:27:44 PM (16 years ago)

Author:

Conrad Huang

Comment:

--

Scripts/MMTK

@@ -27 +27 @@
 To follow the progress of a molecular dynamics run, we can create a Chimera molecule from the MMTK universe and update its atomic coordinates as simulation progresses.  To keep Chimera interactive, we can run the simulation in the background, and poll for atom coordinates changes every few display frames.  The example code is in [attachment:followMD.py followMD.py], which contains a mix of MMTK and Chimera code.
 
-A more elaborate example, [attachment:plotMD.py plotMD.py], extends the previous example to include a plot of the system potential energy along with updating atomic coordinates.  The additional creates a '''matplotlib''' plot, and registers a callback function that is invoked whenever Chimera atomic coordinates are updated.  The arguments to the callback are (1) the MMTK universe, (2) a mapping from MMTK atoms to Chimera atoms, and (3) an MMTK state (which is '''None''' when the callback is invoked after the simulation ends).  The execution of plotMD.py is shown in [attachment:plotMD.mp4 plotMD.mp4].
+A more elaborate example, [attachment:plotMD.py plotMD.py], extends the previous example to include a plot of the system potential energy along with updating atomic coordinates.  The additional creates a '''matplotlib''' plot, and registers a callback function that is invoked whenever Chimera atomic coordinates are updated.  The arguments to the callback are (1) the MMTK universe, (2) a mapping from MMTK atoms to Chimera atoms, and (3) an MMTK state (which is '''None''' when the callback is invoked after the simulation ends).  The execution of plotMD.py is shown in [attachment:plotMD.mp4 plotMD.mp4].  Note that Chimera remains interactive (user is able to select, move and color atoms) throughout the entire MD simulation.
 
 == Caveats ==