Index

A

Adam_box (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute)

Adam_GCMC (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute)

B

bar_U_all() (grandfep.utils.FreeEAnalysis method) BaseGrandCanonicalMonteCarloSampler (class in grandfep.sampler)

box_vectors (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute)

C

calc_neighbor_only (grandfep.utils.md_params_yml attribute) check_ghost_list() (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) check_switching() (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) check_temperature() (grandfep.sampler.NPTSampler method) (grandfep.sampler.NPTSamplerMPI method) chemical_potential (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) comm (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) (grandfep.sampler.NPTSamplerMPI attribute)

compound_integrator (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) custom_nonbonded_force_list (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) customise_force_amber() (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) customise_force_charmm() (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) customise_force_hybrid() (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method)

D

dcd_reporter (class in grandfep.utils) dcd_reporter_dict (grandfep.sampler.NPTSampler attribute) (grandfep.sampler.NPTSamplerMPI attribute)

dt (grandfep.utils.md_params_yml attribute)

E

ex_potential (grandfep.utils.md_params_yml attribute)

F

find_mapping() (in module grandfep.utils)

find_reference_atom_indices() (in module grandfep.utils) FreeEAnalysis (class in grandfep.utils)

G

gen_temp (grandfep.utils.md_params_yml attribute) gen_vel (grandfep.utils.md_params_yml attribute) get_ghost_list() (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) get_lambda_dict() (grandfep.utils.md_params_yml method) get_particle_parameter_index_cust_nb_force() (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler static method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler static method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI static method) get_particle_parameter_offset_dict() (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method)

get_sphere_center() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) get_system_setting() (grandfep.utils.md_params_yml method) get_water_state() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) ghost_list (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) grandfep.utils module

I

init_lambda_state (grandfep.utils.md_params_yml attribute)

integrator (grandfep.utils.md_params_yml attribute)

K

kBT (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) (grandfep.sampler.NPTSampler attribute) (grandfep.sampler.NPTSamplerMPI attribute)

L

lambda_angles (grandfep.utils.md_params_yml attribute) lambda_bonds (grandfep.utils.md_params_yml attribute) lambda_dict (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) (grandfep.sampler.NPTSamplerMPI attribute) lambda_electrostatics_core (grandfep.utils.md_params_yml attribute) lambda_electrostatics_delete (grandfep.utils.md_params_yml attribute) lambda_electrostatics_insert (grandfep.utils.md_params_yml attribute) lambda_gc_coulomb (grandfep.utils.md_params_yml attribute) lambda_gc_vdw (grandfep.utils.md_params_yml attribute) lambda_state_index (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) (grandfep.sampler.NPTSamplerMPI attribute) lambda_states_list (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) (grandfep.sampler.NPTSamplerMPI attribute) lambda_sterics_core (grandfep.utils.md_params_yml attribute)

lambda_sterics_delete (grandfep.utils.md_params_yml attribute) lambda_sterics_insert (grandfep.utils.md_params_yml attribute) lambda_torsions (grandfep.utils.md_params_yml attribute) load_rst() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) (grandfep.sampler.NPTSampler method) (grandfep.sampler.NPTSamplerMPI method) load_sys() (in module grandfep.utils) load_top() (in module grandfep.utils) logger (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) (grandfep.sampler.NPTSampler attribute) (grandfep.sampler.NPTSamplerMPI attribute)

M

maxh (grandfep.utils.md_params_yml attribute) mbar_U_all() (grandfep.utils.FreeEAnalysis method) md_gc_re_protocol (grandfep.utils.md_params_yml attribute) md_params_yml (class in grandfep.utils) module grandfep.utils move_deletion_box() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method)

move_deletion_GCMC() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) move_insert_delete() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) move_insertion_box() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) move_insertion_GCMC() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method)

N

n_lambda_states (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) (grandfep.sampler.NPTSamplerMPI attribute) n_propagation (grandfep.utils.md_params_yml attribute) ncycle_csv (grandfep.utils.md_params_yml attribute) ncycle_dcd (grandfep.utils.md_params_yml attribute) nonbonded_force (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) NoneqGrandCanonicalMonteCarloSampler (class in grandfep.sampler)

NoneqGrandCanonicalMonteCarloSamplerMPI (class in grandfep.sampler) NPTSampler (class in grandfep.sampler) NPTSamplerMPI (class in grandfep.sampler) nst_csv (grandfep.utils.md_params_yml attribute) nst_dcd (grandfep.utils.md_params_yml attribute) nsteps (grandfep.utils.md_params_yml attribute) nstpcouple (grandfep.utils.md_params_yml attribute) num_of_points_water (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute)

P

pcoupltype (grandfep.utils.md_params_yml attribute) prepare_atom_map() (in module grandfep.utils)

prepare_restraints_force() (in module grandfep.utils) print_res_all() (grandfep.utils.FreeEAnalysis static method) print_uncorrelate() (grandfep.utils.FreeEAnalysis method)

R

random_place_water() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) random_rotation_matrix() (in module grandfep.utils) random_rotation_matrix_protoms() (in module grandfep.utils) rank (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) (grandfep.sampler.NPTSamplerMPI attribute) re_step (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) (grandfep.sampler.NPTSamplerMPI attribute) read_energy() (grandfep.utils.FreeEAnalysis static method) ref_p (grandfep.utils.md_params_yml attribute) ref_t (grandfep.utils.md_params_yml attribute) reference_atoms (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) replica_exchange() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) (grandfep.sampler.NPTSamplerMPI method) replica_exchange_global_param() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) (grandfep.sampler.NPTSamplerMPI method) report_dcd() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) (grandfep.sampler.NPTSampler method) (grandfep.sampler.NPTSamplerMPI method)

report_dcd_rank0() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) (grandfep.sampler.NPTSamplerMPI method) report_jsonl() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) report_positions() (grandfep.utils.dcd_reporter method) report_positions_velocities() (grandfep.utils.rst7_reporter method) report_rst() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) (grandfep.sampler.NPTSampler method) (grandfep.sampler.NPTSamplerMPI method) report_rst_rank0() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) (grandfep.sampler.NPTSamplerMPI method) restraint (grandfep.utils.md_params_yml attribute) restraint_fc (grandfep.utils.md_params_yml attribute) rst7_reporter (class in grandfep.utils) rst_reporter_dict (grandfep.sampler.NPTSampler attribute) (grandfep.sampler.NPTSamplerMPI attribute)

S

seconds_to_hms() (in module grandfep.utils) set_ghost_from_jsonl() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) set_ghost_list() (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) set_lambda_dict() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) (grandfep.sampler.NPTSamplerMPI method) set_lambda_state() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) (grandfep.sampler.NPTSamplerMPI method) set_re_step() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) (grandfep.sampler.NPTSamplerMPI method) set_re_step_from_log() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) (grandfep.sampler.NPTSamplerMPI method) set_temperature() (grandfep.utils.FreeEAnalysis method) simulation (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) (grandfep.sampler.NPTSampler attribute) (grandfep.sampler.NPTSamplerMPI attribute)

size (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) (grandfep.sampler.NPTSamplerMPI attribute) sphere_radius (grandfep.utils.md_params_yml attribute) standard_volume (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) (grandfep.utils.md_params_yml attribute) sub_sample() (grandfep.utils.FreeEAnalysis method) surface_tension (grandfep.utils.md_params_yml attribute) switching_water (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) system (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) (grandfep.sampler.NPTSampler attribute) (grandfep.sampler.NPTSamplerMPI attribute) system_setting (grandfep.utils.md_params_yml attribute) system_type (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute)

T

tau_t (grandfep.utils.md_params_yml attribute) temperature (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) (grandfep.sampler.NPTSampler attribute) (grandfep.sampler.NPTSamplerMPI attribute)

topology (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) (grandfep.sampler.NPTSampler attribute) (grandfep.sampler.NPTSamplerMPI attribute)

U

update_gc_count() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method)

W

wat_params (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) water_res_2_atom (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute)

water_res_2_O (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler attribute) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI attribute) work_process() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method)