MPEG animations of the MD simulations were created with the Advanced
Visualization System (AVS) from AVS, Inc.
To animate a simulation, the XYZ files were split into separate files for each
atomic type, in order to be rendered in different colors and radii. For
animation purposes, the atoms were generally divided into three types: all
carbons (white), the hydrogens on one gear (blue), and the hydrogens on the
other gear (green). AVS "field files" (AVS-specific files containing
information on how to interpret the XYZ datasets) were created for each time
step. These were sequentially input to a custom
AVS network (i.e. application) which, for each atomic type,
rendered spheres at the given locations with appropriate radii and the chosen
colors for the atomic types. As each time step was rendered, it was saved as
an X bitmap image. The resultant images were then converted to RGB images, and
then to an MPEG animation using readily-available UNIX utilities.
WebWork: Glenn Deardorff