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grand : Grand Canonical Sampling of Waters in OpenMM
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A
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B
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C
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D
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G
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I
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M
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N
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P
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R
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S
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W
_
__init__() (grand.samplers.BaseGrandCanonicalMonteCarloSampler method)
(grand.samplers.GCMCSphereSampler method)
(grand.samplers.GCMCSystemSampler method)
(grand.samplers.NonequilibriumGCMCSphereSampler method)
(grand.samplers.NonequilibriumGCMCSystemSampler method)
(grand.samplers.StandardGCMCSphereSampler method)
(grand.samplers.StandardGCMCSystemSampler method)
A
add_ghosts() (in module grand.utils)
adjustSpecificWater() (grand.samplers.BaseGrandCanonicalMonteCarloSampler method)
align_traj() (in module grand.utils)
B
BaseGrandCanonicalMonteCarloSampler (class in grand.samplers)
C
calc_mu_ex() (in module grand.potential)
calc_std_volume() (in module grand.potential)
cluster_waters() (in module grand.utils)
create_ligand_xml() (in module grand.utils)
customiseForces() (grand.samplers.BaseGrandCanonicalMonteCarloSampler method)
D
deleteGhostWaters() (grand.samplers.BaseGrandCanonicalMonteCarloSampler method)
deleteRandomWater() (grand.samplers.GCMCSphereSampler method)
(grand.samplers.GCMCSystemSampler method)
deleteWatersInGCMCSphere() (grand.samplers.GCMCSphereSampler method)
deletionMove() (grand.samplers.NonequilibriumGCMCSphereSampler method)
(grand.samplers.NonequilibriumGCMCSystemSampler method)
(grand.samplers.StandardGCMCSphereSampler method)
(grand.samplers.StandardGCMCSystemSampler method)
G
GCMCSphereSampler (class in grand.samplers)
GCMCSystemSampler (class in grand.samplers)
get_data_file() (in module grand.utils)
get_lambda_values() (in module grand.potential)
getReferenceAtomIndices() (grand.samplers.GCMCSphereSampler method)
getSphereCentre() (grand.samplers.GCMCSphereSampler method)
getWaterParameters() (grand.samplers.BaseGrandCanonicalMonteCarloSampler method)
getWaterResids() (grand.samplers.BaseGrandCanonicalMonteCarloSampler method)
getWaterStatusResids() (grand.samplers.BaseGrandCanonicalMonteCarloSampler method)
getWaterStatusValue() (grand.samplers.BaseGrandCanonicalMonteCarloSampler method)
grand.potential
module
grand.samplers
module
grand.utils
module
I
initialise() (grand.samplers.GCMCSphereSampler method)
(grand.samplers.GCMCSystemSampler method)
insertionMove() (grand.samplers.NonequilibriumGCMCSphereSampler method)
(grand.samplers.NonequilibriumGCMCSystemSampler method)
(grand.samplers.StandardGCMCSphereSampler method)
(grand.samplers.StandardGCMCSystemSampler method)
insertRandomWater() (grand.samplers.GCMCSphereSampler method)
(grand.samplers.GCMCSystemSampler method)
M
module
grand.potential
grand.samplers
grand.utils
move() (grand.samplers.BaseGrandCanonicalMonteCarloSampler method)
(grand.samplers.NonequilibriumGCMCSphereSampler method)
(grand.samplers.NonequilibriumGCMCSystemSampler method)
(grand.samplers.StandardGCMCSphereSampler method)
(grand.samplers.StandardGCMCSystemSampler method)
N
NonequilibriumGCMCSphereSampler (class in grand.samplers)
NonequilibriumGCMCSystemSampler (class in grand.samplers)
P
PDBRestartReporter (class in grand.utils)
R
raiseError() (grand.samplers.BaseGrandCanonicalMonteCarloSampler method)
random_rotation_matrix() (in module grand.utils)
read_ghosts_from_file() (in module grand.utils)
read_prepi() (in module grand.utils)
recentre_traj() (in module grand.utils)
remove_ghosts() (in module grand.utils)
report() (grand.samplers.BaseGrandCanonicalMonteCarloSampler method)
(grand.samplers.GCMCSphereSampler method)
(grand.utils.PDBRestartReporter method)
reset() (grand.samplers.BaseGrandCanonicalMonteCarloSampler method)
(grand.samplers.NonequilibriumGCMCSphereSampler method)
(grand.samplers.NonequilibriumGCMCSystemSampler method)
S
setWaterStatus() (grand.samplers.BaseGrandCanonicalMonteCarloSampler method)
shift_ghost_waters() (in module grand.utils)
StandardGCMCSphereSampler (class in grand.samplers)
StandardGCMCSystemSampler (class in grand.samplers)
U
updateGCMCSphere() (grand.samplers.GCMCSphereSampler method)
W
wrap_waters() (in module grand.utils)
write_conect() (in module grand.utils)
write_sphere_traj() (in module grand.utils)
writeGhostWaterResids() (grand.samplers.BaseGrandCanonicalMonteCarloSampler method)
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