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)#
- 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)#