blues
latest
Introduction
Github
Publication
Theory
Installation
Stable Releases
Source Installation
Modules
Moves
Move
RandomLigandRotationMove
MoveEngine
Under Development
Simulation
SystemFactory
SimulationFactory
BLUESSimulation
Integrators
Utilities
Reporters
Formats
Tutorial
Introduction to BLUES
Background
Coupling MD simulations with random NCMC moves for enhanced sampling of ligand binding modes via BLUES
YAML Configuration
Input/Output
Output files
Input files to generate the structure of your system
Restart files
System configuration
(Optional) Hydrogen mass repartitioning
(Optional) Alchemical system configuration
Simulation Configuration
NPT Simulation
(Optional) Additional relaxation steps in the NCMC simulation
(Optional) Platform Properties
Reporter Configuration
(Optional) Advanced options to the
``traj_netcdf``
reporter
Running a BLUES simulation
Selecting a move and initialize the move engine
Generating the Systems for openMM:
``SystemFactory``
(Optional) Applying restraints or freezing atoms
Generating the OpenMM Simulations:
``SimulationFactory``
Run the BLUES Simulation
blues
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Index
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A
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B
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C
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D
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F
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G
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I
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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W
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Z
_
_acceptRejectMove() (blues.simulation.BLUESSimulation method)
_computeAlchemicalCorrection() (blues.simulation.BLUESSimulation method)
_kinetic_energy (blues.integrators.AlchemicalExternalLangevinIntegrator attribute)
_printSimulationTiming() (blues.simulation.BLUESSimulation method)
_resetSimulations() (blues.simulation.BLUESSimulation method)
_setStateTable() (blues.simulation.BLUESSimulation method)
_stepMD() (blues.simulation.BLUESSimulation method)
_stepNCMC() (blues.simulation.BLUESSimulation method)
_syncStatesMDtoNCMC() (blues.simulation.BLUESSimulation method)
A
add_alchemicalLambda() (blues.formats.NetCDF4Traj method)
add_protocolWork() (blues.formats.NetCDF4Traj method)
addBarostat() (blues.simulation.SimulationFactory class method)
addLoggingLevel() (in module blues.reporters)
afterMove() (blues.moves.Move method)
AlchemicalExternalLangevinIntegrator (class in blues.integrators)
alchemicalLambda() (blues.formats.NetCDF4Traj property)
all_atoms (blues.moves.SideChainMove attribute)
amber_selection_to_atomidx() (blues.simulation.SystemFactory static method)
atom_indices (blues.moves.RandomLigandRotationMove attribute)
atomidx_to_atomlist() (blues.simulation.SystemFactory static method)
atomIndexfromTop() (in module blues.utils)
attachReporters() (blues.simulation.SimulationFactory static method)
B
beforeMove() (blues.moves.Move method)
blues.formats
module
blues.integrators
module
blues.moves
module
blues.reporters
module
blues.simulation
module
blues.utils
module
BLUESHDF5Reporter (class in blues.reporters)
BLUESHDF5TrajectoryFile (class in blues.formats)
BLUESSimulation (class in blues.simulation)
BLUESStateDataReporter (class in blues.reporters)
C
calculateNCMCSteps() (in module blues.utils)
center_of_mass (blues.moves.RandomLigandRotationMove attribute)
check_amber_selection() (in module blues.utils)
chooseBondandTheta() (blues.moves.SideChainMove method)
CombinationMove (class in blues.moves)
D
dartsFromParmEd() (blues.moves.SmartDartMove method)
describeNextReport() (blues.reporters.BLUESHDF5Reporter method)
(blues.reporters.BLUESStateDataReporter method)
(blues.reporters.NetCDF4Reporter method)
F
findHeavyRotBonds() (blues.moves.SideChainMove method)
flush() (blues.formats.NetCDF4Traj method)
format() (blues.formats.LoggerFormatter method)
freeze_atoms() (blues.simulation.SystemFactory class method)
freeze_radius() (blues.simulation.SystemFactory class method)
G
generateAlchSystem() (blues.simulation.SystemFactory class method)
generateIntegrator() (blues.simulation.SimulationFactory class method)
generateNCMCIntegrator() (blues.simulation.SimulationFactory class method)
generateSimFromStruct() (blues.simulation.SimulationFactory class method)
generateSimulationSet() (blues.simulation.SimulationFactory method)
generateSystem() (blues.simulation.SystemFactory class method)
get_data_filename() (in module blues.utils)
getAtomIndices() (blues.moves.RandomLigandRotationMove method)
getBackboneAtoms() (blues.moves.SideChainMove method)
getCenterOfMass() (blues.moves.RandomLigandRotationMove method)
getIntegratorInfo() (blues.simulation.BLUESSimulation class method)
getMasses() (blues.moves.RandomLigandRotationMove method)
getRotAtoms() (blues.moves.SideChainMove method)
getRotBondAtoms() (blues.moves.SideChainMove method)
getStateFromContext() (blues.simulation.BLUESSimulation class method)
getTargetAtoms() (blues.moves.SideChainMove method)
I
init_logger() (in module blues.reporters)
initializeSystem() (blues.moves.Move method)
L
LoggerFormatter (class in blues.formats)
M
makeReporters() (blues.reporters.ReporterConfig method)
masses (blues.moves.RandomLigandRotationMove attribute)
module
blues.formats
blues.integrators
blues.moves
blues.reporters
blues.simulation
blues.utils
molecule (blues.moves.SideChainMove attribute)
Move (class in blues.moves)
move() (blues.moves.CombinationMove method)
(blues.moves.Move method)
(blues.moves.RandomLigandRotationMove method)
(blues.moves.SideChainMove method)
(blues.moves.SmartDartMove method)
move_name (blues.moves.MoveEngine attribute)
MoveEngine (class in blues.moves)
moves (blues.moves.MoveEngine attribute)
N
NetCDF4Reporter (class in blues.reporters)
NetCDF4Traj (class in blues.formats)
O
open_new() (blues.formats.NetCDF4Traj class method)
P
parse_unit_quantity() (in module blues.utils)
positions (blues.moves.RandomLigandRotationMove attribute)
print_host_info() (in module blues.utils)
probabilities (blues.moves.MoveEngine attribute)
protocolWork() (blues.formats.NetCDF4Traj property)
Q
qry_atoms (blues.moves.SideChainMove attribute)
R
RandomLigandRotationMove (class in blues.moves)
report() (blues.reporters.BLUESHDF5Reporter method)
(blues.reporters.BLUESStateDataReporter method)
(blues.reporters.NetCDF4Reporter method)
ReporterConfig (class in blues.reporters)
reset() (blues.integrators.AlchemicalExternalLangevinIntegrator method)
residue_list (blues.moves.SideChainMove attribute)
resname (blues.moves.RandomLigandRotationMove attribute)
restrain_positions() (blues.simulation.SystemFactory class method)
rot_atoms (blues.moves.SideChainMove attribute)
rot_bonds (blues.moves.SideChainMove attribute)
rotation_matrix() (blues.moves.SideChainMove method)
run() (blues.simulation.BLUESSimulation method)
runEngine() (blues.moves.MoveEngine method)
S
saveSimulationFrame() (in module blues.utils)
selected_move (blues.moves.MoveEngine attribute)
selectMove() (blues.moves.MoveEngine method)
setContextFromState() (blues.simulation.BLUESSimulation class method)
SideChainMove (class in blues.moves)
SimulationFactory (class in blues.simulation)
SmartDartMove (class in blues.moves)
spreadLambdaProtocol() (in module blues.utils)
structure (blues.moves.RandomLigandRotationMove attribute)
(blues.moves.SideChainMove attribute)
SystemFactory (class in blues.simulation)
T
topology (blues.moves.RandomLigandRotationMove attribute)
totalmass (blues.moves.RandomLigandRotationMove attribute)
W
write() (blues.formats.BLUESHDF5TrajectoryFile method)
Z
zero_masses() (in module blues.utils)
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