PYCV: a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python
Toni Giorgino · The Journal of Open Source Software · 2019
Collective variables (CVs) are functions of the coordinates of particles in a molecular system.The choice of CV is crucial to capture relevant degrees of freedom of the model being simulated (Barducci, Bonomi, & Parrinello, 2011).This is especially important when employing biased sampling techniques such as umbrella sampling or metadynamics (Laio & Parrinello, 2002;Torrie & Valleau, 1977), which apply generalized forces to CVs to enhance the sampling of events otherwise not observable by direct simulation.CVs may be simple geometrical observables (distances, angles, torsions, etc.), but often they are more complex functions designed to capture structural determinants, such as tertiary and quaternary structure of proteins, experimental observables, crystal symmetries, etc. (