acemd.acemd module

class acemd.acemd.FGROUPS(value)

Bases: Enum

An enumeration.

ANGLES = 1

BAROSTAT = 14

BONDS = 0

CMAP = 5

DEBUG = 18

DIHEDRALS = 2

EXTERNAL = 19

IMPLICIT = 16

IMPROPER = 4

NNP = 17

NONBONDED = 11

PLUMED = 15

UREYBRADLEY = 3

acemd.acemd.acemd(directory: Path, inputfile=None, dump_simulation_xml=False, **kwargs)

Run an ACEMD molecular-dynamics simulation in a directory.

Reads an input file (YAML or JSON) from directory, optionally overrides any input-file option via kwargs, runs minimization (if minimize > 0) followed by the production loop, and writes trajectory, log, and restart files into directory.

Parameters:

• directory (Path) – Working directory. The input file, structure / parameters / coordinates referenced by it, and all simulation output live here.

• inputfile (str or Path, optional) – Name of the input file inside directory. If None, input.yaml (or input.json) is auto-detected.

• dump_simulation_xml (bool, optional) – Write the fully constructed OpenMM System to simulation.xml for inspection / debugging.

• **kwargs – Any input-file option (lowercase) or CLI flag, overriding the corresponding value from inputfile. See the ACEMD documentation for the full option list.

Returns:

simulation – The simulation object after the run completes.

Return type:

openmm.app.Simulation

Examples

>>> from acemd import acemd
>>> acemd("/tmp/my_simulation")
>>> acemd("/tmp/my_simulation", run="2ns", device=[0, 1])

acemd.acemd.find_file(filename: str | None, directory: Path)

acemd.acemd.get_acemd_system(directory: Path, inputfile=None, include_extforces=False, set_velocities=False, **kwargs)

acemd.acemd.get_energy_decomposition(context, state)

acemd.acemd.get_sim_properties(context, totalMass, dof)

acemd.acemd.load_molecule(filename, mol=None)

acemd.acemd.print_energy_decomposition(energy_terms)

acemd.acemd.run(directory, simulation, nsteps: int = 0, extforces: list = (), period=25000, velocities=298.15, dump_simulation_xml=False, stepzero=False)

acemd.acemd.setup_acemd(platform: str = 'CUDA', device: list[int] | None = None, precision: str = 'mixed', structure: Path | None = None, pme: bool = True, cutoff: float = 9.0, switching: bool = True, switchdistance: float = 7.5, implicitsolvent: bool = False, igb: int = 2, extforces: list[str] | None = None, fbrefcoor: Path | None = None, plumedfile: Path | None = None, coordinates: Path | None = None, boxsize: list[float] | Path | None = None, velocities: Path | float | None = 298.15, timestep: float = 4.0, slowperiod: int = 1, thermostat: bool = False, thermostattemperature: float = 298.15, thermostatdamping: float = 1, barostat: bool = False, barostatpressure: float = 1.0, barostatanisotropic: bool = False, barostatconstratio: bool = False, barostatconstxy: bool = False, trajectoryfile: str = 'output.xtc', trajvelocityfile: str | None = None, trajforcefile: str | None = None, trajectoryperiod: int = 25000, restart: bool = False, parameters: Path | None = None, run=0, minimize=0, directory='.', include_extforces: bool = False, set_velocities: bool = True, stepzero: bool = False, deterministic: bool = False, rfdielectric: float = 78.5, ncpus: int | None = None, nnp: dict | None = None, hydrogenmass: float = 4.032, hmr: bool | None = None, hbondconstr: bool | None = None, rigidwater: bool | None = None, molecules: dict | None = None, protonate: bool | float = False)

acemd.acemd.setup_barostat(thermostat, barostatanisotropic, barostatconstratio, barostatconstxy, barostatpressure, thermostattemperature, system)