Hyperdynamics¶

The hyperdynamics method uses a bias potential which should be zero at transition states and positive in minima in order to accelerate the rate of transitions. 1 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, 2 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 setting the bias_potential option. It should be run with the parallel_replica job.

[Hyperdynamics] Options¶

bias_potential:

default: none

options:

bond_boost: bond boost method

none: with no bias potential, run regular MD

bb_dvmax:

default: 0.0

The magnitude of the bond-boost bias potential.

bb_rmd_time:

default: 100.0

Regular MD duration used to determine the equilibrium bond length before the bias potential is added.

bb_rcut:

default: 3.0

All bonds which belong to the tagged atoms and are shorter than a cutoff of rcut will be included in the bond-boost potential.

bb_stretch_threshold:

default: 0.2

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

bb_ds_curvature:

default: 0.95

The curvature near the bond-boost dividing surface, it should has a value <= 1. We recommend the value to be 0.9-0.98.

References

1

A.F. Voter “Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events” Phys. Rev. Lett. 78, 3908 (1997)

2

R.A. Miron and K.A. Fichthorn “Accelerated molecular-dynamics of rare events with the bond-boost method” J. Chem. Phys. 119, 6210 (2003)