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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