Simulation and Umbrella sampling ===

• oxdna simulation module
  • Simulation
    • Simulation.build()
    • Simulation.input_file()
    • Simulation.add_protein_par()
    • Simulation.add_force_file()
    • Simulation.add_force()
    • Simulation.add_observable()
    • Simulation.make_sequence_dependant()
  • SimulationManager
    • SimulationManager.queue_sim()
    • SimulationManager.worker_manager()
    • SimulationManager.run()
    • SimulationManager.start_nvidia_cuda_mps_control()
  • GenerateReplicas
    • GenerateReplicas.multisystem_replica()
    • GenerateReplicas.concat_all_system_traj()
  • OxdnaAnalysisTools
    • OxdnaAnalysisTools.align()
    • OxdnaAnalysisTools.centroid()
    • OxdnaAnalysisTools.decimate()
    • OxdnaAnalysisTools.deviations()
    • OxdnaAnalysisTools.mean()
    • OxdnaAnalysisTools.minify()
    • OxdnaAnalysisTools.oxDNA_PDB()
    • OxdnaAnalysisTools.pca()
    • OxdnaAnalysisTools.conformational_entropy()
    • OxdnaAnalysisTools.radius_of_gyration()
    • OxdnaAnalysisTools.subset_trajectory()
    • OxdnaAnalysisTools.com_distance()
    • OxdnaAnalysisTools.angle()
    • OxdnaAnalysisTools.determine_cv_sign()
  • Analysis
    • Analysis.get_init_conf()
    • Analysis.get_last_conf()
    • Analysis.view_init()
    • Analysis.view_last()
    • Analysis.get_conf_count()
    • Analysis.get_conf()
    • Analysis.current_step()
    • Analysis.view_conf()
    • Analysis.plot_energy()
  • Force
    • Force.morse()
    • Force.skew_force()
    • Force.com_force()
    • Force.mutual_trap()
    • Force.string()
    • Force.harmonic_trap()
    • Force.rotating_harmonic_trap()
    • Force.repulsion_plane()
    • Force.repulsion_sphere()
  • Observable
    • Observable.distance()
    • Observable.hb_list()
    • Observable.particle_position()
    • Observable.potential_energy()
    • Observable.force_energy()
    • Observable.kinetic_energy()
• umbrella sampling module
  • BaseUmbrellaSampling
    • BaseUmbrellaSampling.wham_run()
  • ComUmbrellaSampling
    • ComUmbrellaSampling.build_equlibration_runs()
    • ComUmbrellaSampling.build_production_runs()
    • ComUmbrellaSampling.umbrella_forces()
    • ComUmbrellaSampling.rate_umbrella_forces()
  • WhamAnalysis
    • WhamAnalysis.run_wham()
    • WhamAnalysis.chunk_convergence_analysis()
    • WhamAnalysis.data_truncated_convergence_analysis()
    • WhamAnalysis.convergence_analysis()