physical_validation
stable
User guide:
Introduction
Installation
Simulation data
Kinetic energy validation
Ensemble validation
Integrator Validation
Examples:
Kinetic energy distribution
Ensemble check
Kinetic energy equipartition
Integrator validation
Check ensemble of OpenMM temperature replica exchange simulations
Data format and parsers:
Creation of
SimulationData
objects
Data contained in
SimulationData
objects
Package reference:
physical_validation package
physical_validation.data subpackage
physical_validation.util subpackage
physical_validation
»
Index
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Index
B
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C
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D
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E
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F
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G
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I
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K
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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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R
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S
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T
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U
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V
|
W
B
bonds (physical_validation.data.system_data.SystemData property)
bootstrap() (in module physical_validation.util.trajectory)
box (physical_validation.data.trajectory_data.RectangularBox property)
C
calc_molec_kinetic_energy() (in module physical_validation.util.kinetic_energy)
calc_ndof() (in module physical_validation.util.kinetic_energy)
calculate_rmsd() (in module physical_validation.util.integrator)
check() (in module physical_validation.ensemble)
check_1d() (in module physical_validation.util.ensemble)
check_2d() (in module physical_validation.util.ensemble)
check_bins() (in module physical_validation.util.ensemble)
check_convergence() (in module physical_validation.util.integrator)
check_distribution() (in module physical_validation.util.kinetic_energy)
check_equipartition() (in module physical_validation.util.kinetic_energy)
check_mean_std() (in module physical_validation.util.kinetic_energy)
checkensemble_solver() (in module physical_validation.util.ensemble)
chemical_potential_energy() (in module physical_validation.util.ensemble)
compatible() (physical_validation.data.simulation_data.SimulationData static method)
constant_of_motion (physical_validation.data.observable_data.ObservableData property)
constrained_bonds (physical_validation.data.system_data.SystemData property)
convergence() (in module physical_validation.integrator)
cut_tails() (in module physical_validation.util.trajectory)
D
decorrelate() (in module physical_validation.util.trajectory)
distribution() (in module physical_validation.kinetic_energy)
do_linear_fit() (in module physical_validation.util.ensemble)
do_max_likelihood_fit() (in module physical_validation.util.ensemble)
double (physical_validation.util.gromacs_interface.GromacsInterface property)
dt (physical_validation.data.simulation_data.SimulationData property)
E
energy (physical_validation.data.ensemble_data.EnsembleData property)
energy_conversion (physical_validation.data.unit_data.UnitData property)
energy_str (physical_validation.data.unit_data.UnitData property)
ensemble (physical_validation.data.ensemble_data.EnsembleData property)
(physical_validation.data.simulation_data.SimulationData property)
EnsembleData (class in physical_validation.data.ensemble_data)
ensembles() (physical_validation.data.ensemble_data.EnsembleData static method)
equilibrate() (in module physical_validation.util.trajectory)
equipartition() (in module physical_validation.kinetic_energy)
estimate_interval() (in module physical_validation.ensemble)
(in module physical_validation.util.ensemble)
exe (physical_validation.util.gromacs_interface.GromacsInterface property)
F
FileFormatError
FlatfileParser (class in physical_validation.data.flatfile_parser)
G
gather() (physical_validation.data.trajectory_data.RectangularBox method)
generate_histograms() (in module physical_validation.util.ensemble)
get_quantities() (physical_validation.util.gromacs_interface.GromacsInterface method)
get_simulation_data() (physical_validation.data.flatfile_parser.FlatfileParser method)
(physical_validation.data.gromacs_parser.GromacsParser method)
(physical_validation.data.parser.Parser method)
GromacsInterface (class in physical_validation.util.gromacs_interface)
GromacsParser (class in physical_validation.data.gromacs_parser)
grompp() (physical_validation.util.gromacs_interface.GromacsInterface method)
group_kinetic_energy() (in module physical_validation.util.kinetic_energy)
group_ndof() (in module physical_validation.util.kinetic_energy)
I
includepath (physical_validation.util.gromacs_interface.GromacsInterface property)
InputError
is_close() (in module physical_validation.util.kinetic_energy)
K
kb (physical_validation.data.unit_data.UnitData property)
kinetic_energy (physical_validation.data.observable_data.ObservableData property)
kinetic_energy_per_molecule (physical_validation.data.observable_data.ObservableData property)
L
length_conversion (physical_validation.data.unit_data.UnitData property)
length_str (physical_validation.data.unit_data.UnitData property)
M
mass (physical_validation.data.system_data.SystemData property)
max_deviation() (in module physical_validation.util.integrator)
mdrun() (physical_validation.util.gromacs_interface.GromacsInterface method)
module
physical_validation
physical_validation.data.ensemble_data
physical_validation.data.flatfile_parser
physical_validation.data.gromacs_parser
physical_validation.data.observable_data
physical_validation.data.parser
physical_validation.data.simulation_data
physical_validation.data.system_data
physical_validation.data.trajectory_data
physical_validation.data.unit_data
physical_validation.ensemble
physical_validation.integrator
physical_validation.kinetic_energy
physical_validation.util.ensemble
physical_validation.util.error
physical_validation.util.gromacs_interface
physical_validation.util.integrator
physical_validation.util.kinetic_energy
physical_validation.util.plot
physical_validation.util.trajectory
molecule_idx (physical_validation.data.system_data.SystemData property)
mu (physical_validation.data.ensemble_data.EnsembleData property)
N
natoms (physical_validation.data.ensemble_data.EnsembleData property)
(physical_validation.data.system_data.SystemData property)
nconstraints (physical_validation.data.system_data.SystemData property)
nconstraints_per_molecule (physical_validation.data.system_data.SystemData property)
ndof_per_molecule (physical_validation.data.system_data.SystemData property)
ndof_reduction_rot (physical_validation.data.system_data.SystemData property)
ndof_reduction_tra (physical_validation.data.system_data.SystemData property)
nframes (physical_validation.data.observable_data.ObservableData property)
number_of_species (physical_validation.data.observable_data.ObservableData property)
O
ObservableData (class in physical_validation.data.observable_data)
observables (physical_validation.data.simulation_data.SimulationData property)
observables() (physical_validation.data.observable_data.ObservableData static method)
overlap() (in module physical_validation.util.trajectory)
P
Parser (class in physical_validation.data.parser)
physical_validation
module
physical_validation.data.ensemble_data
module
physical_validation.data.flatfile_parser
module
physical_validation.data.gromacs_parser
module
physical_validation.data.observable_data
module
physical_validation.data.parser
module
physical_validation.data.simulation_data
module
physical_validation.data.system_data
module
physical_validation.data.trajectory_data
module
physical_validation.data.unit_data
module
physical_validation.ensemble
module
physical_validation.integrator
module
physical_validation.kinetic_energy
module
physical_validation.util.ensemble
module
physical_validation.util.error
module
physical_validation.util.gromacs_interface
module
physical_validation.util.integrator
module
physical_validation.util.kinetic_energy
module
physical_validation.util.plot
module
physical_validation.util.trajectory
module
PhysicalValidationError
plot() (in module physical_validation.util.plot)
position (physical_validation.data.trajectory_data.TrajectoryData property)
potential_energy (physical_validation.data.observable_data.ObservableData property)
prepare() (in module physical_validation.util.trajectory)
pressure (physical_validation.data.ensemble_data.EnsembleData property)
(physical_validation.data.observable_data.ObservableData property)
pressure_conversion (physical_validation.data.unit_data.UnitData property)
pressure_str (physical_validation.data.unit_data.UnitData property)
print_stats() (in module physical_validation.util.ensemble)
pymbar_bar() (in module physical_validation.util.ensemble)
R
raise_if_ensemble_is_invalid() (physical_validation.data.simulation_data.SimulationData method)
raise_if_observable_data_is_invalid() (physical_validation.data.simulation_data.SimulationData method)
raise_if_system_data_is_invalid() (physical_validation.data.simulation_data.SimulationData method)
raise_if_trajectory_data_is_invalid() (physical_validation.data.simulation_data.SimulationData method)
raise_if_units_are_none() (physical_validation.data.simulation_data.SimulationData method)
read_gro() (physical_validation.util.gromacs_interface.GromacsInterface static method)
read_mdp() (physical_validation.util.gromacs_interface.GromacsInterface static method)
read_system_from_top() (physical_validation.util.gromacs_interface.GromacsInterface method)
read_trr() (physical_validation.util.gromacs_interface.GromacsInterface method)
RectangularBox (class in physical_validation.data.trajectory_data)
S
set_ensemble() (physical_validation.data.simulation_data.SimulationData method)
SimulationData (class in physical_validation.data.simulation_data)
system (physical_validation.data.simulation_data.SimulationData property)
SystemData (class in physical_validation.data.system_data)
T
temperature (physical_validation.data.ensemble_data.EnsembleData property)
(physical_validation.data.observable_data.ObservableData property)
temperature_conversion (physical_validation.data.unit_data.UnitData property)
temperature_str (physical_validation.data.unit_data.UnitData property)
test_group() (in module physical_validation.util.kinetic_energy)
time_conversion (physical_validation.data.unit_data.UnitData property)
time_str (physical_validation.data.unit_data.UnitData property)
total_energy (physical_validation.data.observable_data.ObservableData property)
trajectories() (physical_validation.data.trajectory_data.TrajectoryData static method)
trajectory (physical_validation.data.simulation_data.SimulationData property)
TrajectoryData (class in physical_validation.data.trajectory_data)
U
UnitData (class in physical_validation.data.unit_data)
units (physical_validation.data.simulation_data.SimulationData property)
units() (physical_validation.data.gromacs_parser.GromacsParser static method)
(physical_validation.data.unit_data.UnitData class method)
V
velocity (physical_validation.data.trajectory_data.TrajectoryData property)
volume (physical_validation.data.ensemble_data.EnsembleData property)
(physical_validation.data.observable_data.ObservableData property)
volume_conversion (physical_validation.data.unit_data.UnitData property)
volume_str (physical_validation.data.unit_data.UnitData property)
W
write_mdp() (physical_validation.util.gromacs_interface.GromacsInterface static method)
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