Index

A

Adam_box (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute)

Adam_GCMC (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute)

B

BaseGrandCanonicalMonteCarloSampler (class in grandfep.sampler)

C

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)

compound_integrator (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) custom_nonbonded_force (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute)

D

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

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

F

find_reference_atom_indices() (in module grandfep.utils)

G

gcmc_move() (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) get_ghost_list() (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) get_particle_parameter_index_cust_nb_force() (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method)

get_particle_parameter_offset_dict() (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method) ghost_list (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) grandfep.utils module

I

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

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

K

kBT (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute)

L

load_sys() (in module grandfep.utils)

load_top() (in module grandfep.utils) logger (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute)

M

module grandfep.utils

N

nonbonded_force (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) NoneqGrandCanonicalMonteCarloSampler (class in grandfep.sampler)

NoneqGrandCanonicalMonteCarloSamplerMPI (class in grandfep.sampler) num_of_points_water (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute)

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

S

set_ghost_list() (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSampler method) (grandfep.sampler.NoneqGrandCanonicalMonteCarloSamplerMPI method)

simulation (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) switching_water (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) system_type (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute)

T

temperature (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute)

topology (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute)

U

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

W

wat_params (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute)

water_res_2_atom (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute) water_res_2_O (grandfep.sampler.BaseGrandCanonicalMonteCarloSampler attribute)