Metadynamics Example

The aim is to integrate out everything but the dihedral angle (collective variable, a.k.a. reaction coordinate or order parameter) shown in the picture. In other words, the goal is to compute equilibrium probability density of the collective variable, and, thus, the associated free energy (a.k.a. potential of mean force).

1.Regular molecular dynamics

2.Metadynamics

3.Biased molecular dynamics