CHE210D: Principles of modern molecular simulation methods, F19
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Course syllabus and schedule
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Lecture notes


Writing of atomic trajectories to pdb files for import into molecular visualization programs:

A simple molecular dynamics simulation of the Lennard-Jones system:

Weeks 1, 2

Week 3

Weeks 4, 5

Weeks 5, 6
  • read: Statistical mechanics of classical systems and Other ensembles
  • do: Start thinking about a final project topic.
  • assignment: Exercise 4, due 11/7/19
  • related reading: Leach Chapter 8; Frenkel and Smit Chapters 3, 5

Weeks 7, 8

  • assignment: Final project
  • related reading Leach Chapter 11; Frenkel & Smit Chapters 7, 9, 10

Weeks 9, 10

  • assignment: Final project
  • related reading: Leach Chapters 8, 11; Frenkel & Smit Chapters 7, 9, 10

Software to install
Programming exercises in the course will require a Python installation, the NumPy and SciPy add-on libraries for Python, C/C++ and Fortran compilers, and (optionally) a Python script editor.  In this course, examples will use the Python 2.7 series (latest version 2.7.2), not the Python 3 series that breaks compatability with the earlier version of the language.  You are welcome to use Python 3 for your code, however.

Python, a Python editor, plus all of the support libraries that you will need for scientific computing are conveniently combined in the Anaconda Distribution, which is available on Windows, Mac, and Linux platforms.  You can download it for free.  In particular, it includes a nice Python editor called Spyder that you are encouraged to explore and use.

Anaconda installs a default set of Python modules that are generally sufficient for most tasks.  However, as a part of this course we will need to write Fortran code that is much faster for numercally-intense calculations.  The Fortran code can be compiled into Python-importable functions, rather automatically.  To enable such a workflow, you will need to add several additional packages to your Anaconda Installation, which you can do with the Anaconda Navigator:
  • gfortran, an open source Fortran compiler

For Windows machines, you will also need:
  • m2w64-gcc-fortran
  • m2w64-gcc-libgFortran
  • libpython

Department of Chemical Engineering  |  University of California Santa Barbara