acemd.acemd module

class acemd.acemd.FGROUPS(*values)

Bases: Enum

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, 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, directory)

acemd.acemd.get_acemd_system(directory, 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=0, extforces=(), period=25000, velocities=298.15, dump_simulation_xml=False, stepzero=False)

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

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