Course syllabus and
schedule
Download
here.
Software
to install
Base software for the course is listed below. Be sure to grab
the version indicated. Failure to do so may result in incompatibilities.
On Windows
systems, ActivePython requires the following additional file
to work correctly with gfortran and f2py. Unzip the file and
place it in Python25\libs\libpython25.a:
The following Python add-on enables easy, real-time 3D visualization
using Python programming. It is used by the codes provided below to
animate molecular simulations:
Reading
Lecture notes
Codes
Real-time visualization of atomic trajectories (requires VPython):
Writing of atomic trajectories to pdb files for import into molecular
visualization programs:
A simple molecular dynamics simulation of the Lennard-Jones system,
with visualization:
Assignments
Weeks
1, 2
Week
3
Weeks 4, 5
Weeks 5, 6
Weeks 7, 8
- read:
Final project
- book:
Chapter 11 (also Frenkel & Smit Chapters 7, 9, 10)
- do:
Start thinking about a final project topic.
- assignment:
Exercise 5,
due 5/21/09 (optional with final project)
Weeks 9, 10
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