metadynamics.integrate Namespace Reference

Commands to integrate the equation of motion using metadynamics. More...

Classes
class	mode_metadynamics
	Enables integration using metadynamics, a free energy technique. More...

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Detailed Description

Commands to integrate the equation of motion using metadynamics.

This package implements a metadynamics integration mode using an adaptive bias potential.

Metadynamics integration (integrate.mode_metadynamics) can be combined with any standard integration methods, such as NVT, NVE etc. supported by HOOMD-Blue.

In addition to integration methods, metadynamics also requires at least one collective variable (cv) to be defined, the values of which will be sampled to update the bias potential. The forces generated from the bias potential are added to the particles during the simulation.

This package supports well-tempered metadynamics with multiple collective variables, on- and off-grid bias potentials, and saving of and restarting from grid information. It is also possible to simply equilibrate the system in the presence of a previously generated bias potential, without updating the latter, to sample a histogram of values of the collective variable (i.e. for error control)