Index

A

add_consraints() (TIES_MD.alch.AlchSys method) add_simulation_reporters() (in module TIES_MD.alch) AlchemicalStateError AlchSys (class in TIES_MD.alch) amend_original_positions() (TIES_MD.alch.AlchSys method)

Analysis (class in TIES_MD.ties_analysis.ties_analysis) analysis() (TIES_MD.ties_analysis.methods.FEP.MBAR_Analysis method) (TIES_MD.ties_analysis.methods.TI.TI_Analysis method) appear_func() (in module TIES_MD.lambdas) apply_to_context() (TIES_MD.openmmtools.alchemy.ModifiedAlchemicalState method) apply_to_system() (TIES_MD.openmmtools.alchemy.ModifiedAlchemicalState method)

B

build_results_dirs() (TIES_MD.TIES.TIES method)

build_simulation() (TIES_MD.alch.AlchSys method)

C

cell_basis_vec1 (TIES_MD.TIES.TIES property) cell_basis_vec2 (TIES_MD.TIES.TIES property) cell_basis_vec3 (TIES_MD.TIES.TIES property) check_system_consistency() (TIES_MD.openmmtools.alchemy.ModifiedAlchemicalState method)

collate_data() (TIES_MD.ties_analysis.engines.namd.NAMD method) (TIES_MD.ties_analysis.engines.openmm.OpenMM method) compute_bs_error() (in module TIES_MD.ties_analysis.methods.TI) Config (class in TIES_MD.ties_analysis.config)

D

debug_force() (TIES_MD.alch.AlchSys method)

decorrelate_data() (TIES_MD.ties_analysis.methods.FEP.MBAR_Analysis method) disappear_func() (in module TIES_MD.lambdas)

E

elec_edges (TIES_MD.TIES.TIES property)

engine (TIES_MD.TIES.TIES property) equilibriation() (in module TIES_MD.alch)

F

from_system() (TIES_MD.openmmtools.alchemy.ModifiedAlchemicalState class method)

G

get_alchemical_atoms() (in module TIES_MD.alch) get_alchemical_variable() (TIES_MD.openmmtools.alchemy.ModifiedAlchemicalState method) get_box_vectors() (in module TIES_MD.TIES) get_constraints() (in module TIES_MD.alch) get_function_variable() (TIES_MD.openmmtools.alchemy.ModifiedAlchemicalState method) get_gradients() (TIES_MD.alch.AlchSys method) get_header_and_run() (in module TIES_MD.TIES) get_intersect_angles() (TIES_MD.alch.AlchSys method) get_intersect_bonds() (TIES_MD.alch.AlchSys method) get_intersect_torsions() (TIES_MD.alch.AlchSys method)

get_iter() (in module TIES_MD.ties_analysis.engines.namd) get_lam_diff() (in module TIES_MD.ties_analysis.methods.TI) get_line() (in module TIES_MD.lambdas) get_options() (TIES_MD.TIES.TIES method) (TIES_MD.ties_analysis.config.Config method) get_replica() (in module TIES_MD.ties_analysis.engines.namd) (in module TIES_MD.ties_analysis.engines.openmm) get_window() (in module TIES_MD.ties_analysis.engines.namd) (in module TIES_MD.ties_analysis.engines.openmm) global_lambdas (TIES_MD.TIES.TIES property)

I

intergrate() (TIES_MD.ties_analysis.methods.TI.TI_Analysis method)

L

lambda_angles (TIES_MD.openmmtools.alchemy.ModifiedAlchemicalState attribute) lambda_bonds (TIES_MD.openmmtools.alchemy.ModifiedAlchemicalState attribute) lambda_electrostatics (TIES_MD.openmmtools.alchemy.ModifiedAlchemicalState attribute)

lambda_sterics (TIES_MD.openmmtools.alchemy.ModifiedAlchemicalState attribute) lambda_torsions (TIES_MD.openmmtools.alchemy.ModifiedAlchemicalState attribute) Lambdas (class in TIES_MD.lambdas) (class in TIES_MD.ties_analysis.engines.openmm)

M

main() (in module TIES_MD.cli) (in module TIES_MD.ties_analysis.ties_analysis) make_exp() (in module TIES_MD.ties_analysis.ties_analysis) MBAR_Analysis (class in TIES_MD.ties_analysis.methods.FEP) minimization() (in module TIES_MD.alch) ModifiedAbsoluteAlchemicalFactory (class in TIES_MD.openmmtools.alchemy) ModifiedAlchemicalState (class in TIES_MD.openmmtools.alchemy) module TIES_MD TIES_MD.alch TIES_MD.cli TIES_MD.eng_scripts TIES_MD.eng_scripts.cfg_scripts TIES_MD.eng_scripts.namd_sub TIES_MD.eng_scripts.namd_sub_split TIES_MD.eng_scripts.openmm_sub TIES_MD.eng_scripts.openmm_sub_split TIES_MD.lambdas TIES_MD.openmmtools TIES_MD.openmmtools.alchemy TIES_MD.TIES TIES_MD.ties_analysis TIES_MD.ties_analysis.config TIES_MD.ties_analysis.engines TIES_MD.ties_analysis.engines.namd TIES_MD.ties_analysis.engines.openmm TIES_MD.ties_analysis.methods TIES_MD.ties_analysis.methods.FEP TIES_MD.ties_analysis.methods.TI TIES_MD.ties_analysis.ties_analysis

N

NAMD (class in TIES_MD.ties_analysis.engines.namd)

nice_print() (in module TIES_MD.TIES) (in module TIES_MD.ties_analysis.ties_analysis)

O

OpenMM (class in TIES_MD.ties_analysis.engines.openmm)

P

PDB_line (class in TIES_MD.alch) plot_du_by_dl() (TIES_MD.ties_analysis.methods.TI.TI_Analysis method)

plot_overlap_mat() (TIES_MD.ties_analysis.methods.FEP.MBAR_Analysis method) preproduction() (in module TIES_MD.alch)

R

read_alch_file() (in module TIES_MD.ties_analysis.engines.namd) read_config() (in module TIES_MD.TIES) (in module TIES_MD.ties_analysis.config) rebuild_torsion() (TIES_MD.alch.AlchSys method) remove_simulation_reporters() (in module TIES_MD.alch)

replica_analysis() (TIES_MD.ties_analysis.methods.FEP.MBAR_Analysis method) run() (TIES_MD.TIES.TIES method) (TIES_MD.ties_analysis.ties_analysis.Analysis method) run_analysis() (TIES_MD.ties_analysis.engines.namd.NAMD method) (TIES_MD.ties_analysis.engines.openmm.OpenMM method)

S

set_alchemical_parameters() (TIES_MD.openmmtools.alchemy.ModifiedAlchemicalState method) set_alchemical_variable() (TIES_MD.openmmtools.alchemy.ModifiedAlchemicalState method) set_context_to_state() (TIES_MD.alch.AlchSys method) set_function_variable() (TIES_MD.openmmtools.alchemy.ModifiedAlchemicalState method) setup() (TIES_MD.TIES.TIES method)

shift_alchemical_positions() (TIES_MD.alch.AlchSys method) simulate_system() (in module TIES_MD.alch) split_run (TIES_MD.TIES.TIES property) ster_edges (TIES_MD.TIES.TIES property) System_ID (class in TIES_MD.alch)

T

test_sim() (TIES_MD.alch.AlchSys method) TI_Analysis (class in TIES_MD.ties_analysis.methods.TI) TIES (class in TIES_MD.TIES) TIES_MD module TIES_MD.alch module TIES_MD.cli module TIES_MD.eng_scripts module TIES_MD.eng_scripts.cfg_scripts module TIES_MD.eng_scripts.namd_sub module TIES_MD.eng_scripts.namd_sub_split module TIES_MD.eng_scripts.openmm_sub module TIES_MD.eng_scripts.openmm_sub_split module TIES_MD.lambdas module

TIES_MD.openmmtools module TIES_MD.openmmtools.alchemy module TIES_MD.TIES module TIES_MD.ties_analysis module TIES_MD.ties_analysis.config module TIES_MD.ties_analysis.engines module TIES_MD.ties_analysis.engines.namd module TIES_MD.ties_analysis.engines.openmm module TIES_MD.ties_analysis.methods module TIES_MD.ties_analysis.methods.FEP module TIES_MD.ties_analysis.methods.TI module TIES_MD.ties_analysis.ties_analysis module

U

update_attrs_from_schedule() (TIES_MD.lambdas.Lambdas method) (TIES_MD.ties_analysis.engines.openmm.Lambdas method)

update_cfg() (TIES_MD.TIES.TIES method)

W

write_analysis_cfg() (TIES_MD.TIES.TIES method) write_namd_eq() (TIES_MD.TIES.TIES method) write_namd_min() (TIES_MD.TIES.TIES method)

write_namd_prod() (TIES_MD.TIES.TIES method) write_namd_scripts() (TIES_MD.TIES.TIES method) write_namd_submissions() (TIES_MD.TIES.TIES method) write_openmm_submission() (TIES_MD.TIES.TIES method)