MCCCS Towhee (Algorithm)



    This section contains a series of essays discussing topics related to the algorithms that power the Towhee program.

  • Monte Carlo primer with general background information about the Monte Carlo method. A good place to start if you are relatively new to molecular simulation.
  • Chemical Potential detailed description of the many slightly different flavors of Chemical Potential computed in Towhee. Please read this essay before you attempt a Grand Canonical simulation. Chemical potential of polyatomic molecules is a complex topic and one that leads to a great deal of confusion and mistakes.
  • Configurational-bias Monte Carlo is the primary algorithm used to sample molecule conformations in Towhee.
  • Polymer builder is a discussion about the best ways to use the polymer builder functionality currently built into Towhee (polypeptides and nucleic acids), and also lays out a vision for a more general version of the polymer builder that I would like to see implemented into Towhee in the future.
  • Pressure detailed description of the different algorithms used to compute pressure in Towhee.


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Send comments to: Marcus G. Martin

Last updated: July 25, 2014