Collective Variables

The collective variable in OpenPathSampling is essentially just a wrapper around a function. Developers can extend collective variables in a couple ways. First, is the very simple approach of creating a particular generally useful function which you might like to wrap in an OPS CV. Second is the more complicated idea of creating a general wrapper for a class functions, e.g., from some molecular dynamics analysis library.

The first examples

Wrapping a function in a CV

Under most circumstances, you don’t need to subclass CollectiveVariable. Instead, you should wrap the function you would like to use in an OPS CollectiveVariable.

To do this, you create an instance of FunctionCV.

Creating a wrapper class for a library

OPS doesn’t bother defining any collective variables internally, because we count on other codes to have a wide range and fast implementations. To make it very easy to wrap functions from your favorite libraries in OPS CVs, we create custom classes for various libraries. In particular, OPS supports simple wrapping of MDTraj functions and of pyEmma “featurizers.” If you’d like to extend OPS to support simple wrapping of some other library, this section is for you.