Collective Variables

Collective variables (CVs) are functions that map an MD snapshot to a number. They are typically used to define stable states and interface sets.

CVs can be made under the top-level keyword cvs. The following types are available:

mdtraj

Use an MDTraj analysis function to calculate a CV.

• type - type identifier; must exactly match the string mdtraj (required)

• name (string) - name this object in order to reuse it

• topology (string) - topology from file or engine name (required)

• func (string) - MDTraj function, e.g., compute_distances (required)

• kwargs (dict) - keyword arguments for func

• period_min (EvalFloat) - minimum value for a periodic function, None if not periodic

• period_max (EvalFloat) - maximum value for a periodic function, None if not periodic