TIES_MD

• TIES_MD package
  • Subpackages
    • TIES_MD.eng_scripts package
      • Subpackages
      • Module contents
    • TIES_MD.openmmtools package
      • Submodules
      • TIES_MD.openmmtools.alchemy module
      • Module contents
    • TIES_MD.ties_analysis package
      • Subpackages
      • Submodules
      • TIES_MD.ties_analysis.config module
      • TIES_MD.ties_analysis.ties_analysis module
      • Module contents
  • Submodules
  • TIES_MD.TIES module
    • TIES
      • TIES.build_results_dirs()
      • TIES.cell_basis_vec1
      • TIES.cell_basis_vec2
      • TIES.cell_basis_vec3
      • TIES.elec_edges
      • TIES.engine
      • TIES.get_options()
      • TIES.global_lambdas
      • TIES.run()
      • TIES.setup()
      • TIES.split_run
      • TIES.ster_edges
      • TIES.update_cfg()
      • TIES.write_analysis_cfg()
      • TIES.write_namd_eq()
      • TIES.write_namd_min()
      • TIES.write_namd_prod()
      • TIES.write_namd_scripts()
      • TIES.write_namd_submissions()
      • TIES.write_openmm_submission()
    • get_box_vectors()
    • get_header_and_run()
    • nice_print()
    • read_config()
  • TIES_MD.alch module
    • AlchSys
      • AlchSys.add_consraints()
      • AlchSys.amend_original_positions()
      • AlchSys.build_simulation()
      • AlchSys.debug_force()
      • AlchSys.get_gradients()
      • AlchSys.get_intersect_angles()
      • AlchSys.get_intersect_bonds()
      • AlchSys.get_intersect_torsions()
      • AlchSys.rebuild_torsion()
      • AlchSys.set_context_to_state()
      • AlchSys.shift_alchemical_positions()
      • AlchSys.test_sim()
    • PDB_line
    • System_ID
    • add_simulation_reporters()
    • equilibriation()
    • get_alchemical_atoms()
    • get_constraints()
    • minimization()
    • preproduction()
    • remove_simulation_reporters()
    • simulate_system()
  • TIES_MD.cli module
    • main()
  • TIES_MD.lambdas module
    • Lambdas
      • Lambdas.update_attrs_from_schedule()
    • appear_func()
    • disappear_func()
    • get_line()
  • Module contents