acemd package

Submodules

• acemd.acemd module
  • FGROUPS
    • FGROUPS.ANGLES
    • FGROUPS.BAROSTAT
    • FGROUPS.BONDS
    • FGROUPS.CMAP
    • FGROUPS.DEBUG
    • FGROUPS.DIHEDRALS
    • FGROUPS.EXTERNAL
    • FGROUPS.IMPLICIT
    • FGROUPS.IMPROPER
    • FGROUPS.NNP
    • FGROUPS.NONBONDED
    • FGROUPS.PLUMED
    • FGROUPS.UREYBRADLEY
  • acemd()
  • find_file()
  • get_acemd_system()
  • get_energy_decomposition()
  • get_sim_properties()
  • load_molecule()
  • print_energy_decomposition()
  • run()
  • setup_acemd()
  • setup_barostat()
• acemd.charmm module
  • cleanup_charmm_prm()
• acemd.input module
  • detect_input_file()
  • parse_input_file()
• acemd.licensing module
  • acemd_register()
• acemd.minimizer module
  • bracket_and_golden_section_search()
  • cgmin_compute()
  • get_energy_forces()
  • minimize()
• acemd.nnp module
• acemd.protocols module
  • get_cellular_restraints()
  • setup_equilibration()
  • setup_production()
• acemd.reporters module
  • CustomReporter
    • CustomReporter.describeNextReport()
    • CustomReporter.report()
  • LoggingReporter
    • LoggingReporter.aliases
    • LoggingReporter.aliases2
    • LoggingReporter.describeNextReport()
    • LoggingReporter.field_widths
    • LoggingReporter.report()
  • SpeedLogger
    • SpeedLogger.step()
  • setup_reporters()
• acemd.restraints module
  • PositionalRestraint
    • PositionalRestraint.from_restraint_dict()
    • PositionalRestraint.from_restraint_str()
    • PositionalRestraint.parse_restraint()
    • PositionalRestraint.setupForce()
    • PositionalRestraint.to_dict()
  • get_force_str()
  • parse_setpoint()
  • parse_setpoints()
  • setup_extforces()
  • update_restraints()
• acemd.system module
  • create_forcefield()
  • openmm_to_molecule()
• acemd.utils module
  • plumed_parser()
  • view_forces()
• acemd.versionwarnings module

Module contents