Dynamics
The details of molecular dynamics (MD) simulations are specified here. Not all keywords apply to every available method. Note that there is a fundamental difference in using dynamics to either sample free energies, or as a means to escape local minima in the minima hopping method. For the former, the goal is an accurate and unbiased sampling, while for the latter it is the efficient escape from a catchment basin of the PES. Hence, the available parameters and their suggested values differ significantly between these two classes of dynamics.
dynamics options
md_method: (string) Type of MD simulation ensemble.
default:
No default value.options:
nvt_nose: NVT ensemble with the Nose-Hoover chain thermostat.
nvt_langev: NVT ensemble with the Langevin thermostat.
nve: NVE ensemble (under development).
nmd: (integer) Number of MD steps.
default:
300
nfreq: (integer) The frequency at which detailed output is written to disk.
default:
0
dt: (real) Time step size. Units in fs.
default:
No default value.
temp: (real) Target temperature. In units of Kelvin.
default:
0.d0
init_temp: (real) Initial temperature. In units of Kelvin.
default:
0.d0
highest_freq: (real) Coupling constant to the extended system. Units in \({\textrm{Ha}}/{\textrm{THz}^{2}}\).
default:
1.d1
ntherm: (integer) Number of thermostats used for the Nose-Hoover thermostat chain.
default:
2
restart: (logical) Activates a restart from a previously interrupted MD run.
default:
False
Parameters specifically for the MD escape trials in task minhocao
algo: (integer) Choice of variable cell shape algorithms.
default:
1options:
1: Parrinello-Rahman
2: Cleveland
3: Wentzcovitch
4: Andersen (variable cell volume only, fixed cell shape)
integrator: (integer) Integrator for the variable cell shape MD equations of motion.
default:
3options:
1: Velocity Verlet
2: Classic Verlet
3: Beeman corrector-predictor scheme
presscomp: (real) Sets a bias pressure for MD runs in task minhocao
simulations. The high temperatures in the minhocao cycles
can lead to the cell expanding
significantly beyond the equlibrium volume.
To counteract this thermal expansing,
a bias pressure can be imposed during the MD run.
In units of GPa.
default:
0.d0
cellmass: (real) Fictitious cell mass for all variable cell shape MD tasks. Arbitrary units.
default:
1.d0
mdmin_init: (integer) The initial stopping criterion mdmin
for an MD run in task minhocao.
The MD run is terminated as soon as mdmin minima in the
potential energy/enthalpy along the MD trajectory is encountered.
default:
2
auto_mdmin: (logical) The stopping criterion for an MD run
is adjusted dynamically if True.
mdmin will fluctuate between mdmin_min and mdmin_max.
Used for the MD escape steps in task minhocao.
default:
False
mdmin_min: (integer)
The minimal value of mdmin.
Used for the MD escape steps in task minhocao and if auto_mdmin is True.
default:
2
mdmin_max: (integer)
The maximal value of mdmin.
Used for the MD escape steps in task minhocao and if auto_mdmin is True.
default:
2
auto_mddt: (logical) Activates the dynamical adjustment of the MD
timestep dt in task minhocao. For clusters, dt is adjusted
such that the total energy is conserved to within 1 %,
and has to be accompanied by setting encon to True.
For peridic systems,
dt is adjusted such that the number of sampling points
per oscillation in the energy/enthalpy along an MD trajectory is close to the
target value nit_per_min.
default:
False
encon: (logical) Activates the dynamical adjustment of the MD
timestep dt in task minhocao for clusters
based on energy conservation.
default:
False
nit_per_min: (integer) Target number of MD samples per
energy/enthalpy oscillation. Only used if auto_mddt is True.
default:
25
dt_init: (real) Initial MD time step dt. In atomic units.
default:
2.d1