Hyperdynamics

The hyperdynamics method uses a bias potential which should be zero at transition states and positive in minima to accelerate the rate of transitions as noted by Voter [HD_Vot97].

The hyperdynamics time step \(\delta t\) can be obtained from the molecular dynamics simulation time step \(\delta t^b\) multiplied by a boost factor \(e^{\beta \Delta V}\), where \({\Delta V}\) is the bias potential.

There are several possible forms of bias potential. In eOn, we have implemented the bond-boost method of Miron and Fichthorn [HD_MF03] where the bias potential is controlled by the maximal (fractional) change in any bond length in the system. This is a good bias potential for systems in which the dynamics is governed by bond breaking and forming events.

You can run a hyperdynamics job by:

The client job token is safe_hyperdynamics. hyperdynamics does not name a client job.

Configuration

[Hyperdynamics]
pydantic model eon.schema.HyperdynamicsConfig[source]
Fields:

  • bias_potential (Literal['none', 'bond_boost'])

  • bb_dvmax (float)

  • bb_rmd_time (float)

  • bb_boost_atom_list (str | list[int])

  • bb_rcut (float)

  • bb_stretch_threshold (float)

  • bb_ds_curvature (float)

field bias_potential: Literal['none', 'bond_boost'] = 'none'

Options: - none: With no bias potential, run regular MD. - bond_boost: Bond boost method.

Type of bias potential to use.

field bb_dvmax: float = 0.0

The magnitude of the bond-boost bias potential.

field bb_rmd_time: float = 100.0

Regular MD duration (in fs) to determine equilibrium bond length before adding bias potential.

field bb_boost_atom_list: str | list[int] = 'ALL'

The atoms that will be displaced in the calculation: a comma delimited list of atom indices, e.g. 0,1,2. Default is ‘All’.

field bb_rcut: float = 3.0

Cutoff distance (in Angstroms) for bonds included in the bond-boost potential.

field bb_stretch_threshold: float = 0.2

It should be smaller than the maximum fractional nearest-neighbor bond stretch or compression at any transition state.

Defines the bond-boost dividing surface.

field bb_ds_curvature: float = 0.95

It should have a value <= 1. We recommend the value to be 0.9-0.98.

Curvature near the bond-boost dividing surface.

References

[HD_MF03]

Radu A. Miron and Kristen A. Fichthorn. Accelerated molecular dynamics with the bond-boost method. The Journal of Chemical Physics, 119(12):6210–6216, September 2003. doi:10.1063/1.1603722.

[HD_Vot97]

Arthur F. Voter. Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events. Physical Review Letters, 78(20):3908–3911, May 1997. doi:10.1103/PhysRevLett.78.3908.