BioSimSpace.Protocol.FreeEnergy¶
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class
BioSimSpace.Protocol.
FreeEnergy
(lam=0.0, lam_vals=None, min_lam=0.0, max_lam=1.0, num_lam=11, timestep=2.0000 fs, runtime=4.0000 ns, temperature=300.0000 K, pressure=1.0000 atm, report_interval=200000, restart_interval=20000, perturbation_type='full')¶ A class for storing free energy protocols.
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__init__
(lam=0.0, lam_vals=None, min_lam=0.0, max_lam=1.0, num_lam=11, timestep=2.0000 fs, runtime=4.0000 ns, temperature=300.0000 K, pressure=1.0000 atm, report_interval=200000, restart_interval=20000, perturbation_type='full')¶ Constructor.
- Parameters
lam (float) – The perturbation parameter: [0.0, 1.0]
lam_vals ([float]) – The list of lambda parameters.
min_lam (float) – The minimum lambda value.
max_lam (float) – The maximum lambda value.
num_lam (int) – The number of lambda values.
timestep (
Time
) – The integration timestep.runtime (
Time
) – The running time.temperature (
Temperature
) – The temperature.pressure (
Pressure
) – The pressure. Pass pressure=None to use the NVT ensemble.report_interval (int) – The frequency at which statistics are recorded. (In integration steps.)
restart_interval (int) – The frequency at which restart configurations and trajectory
perturbation_type (str) –
- The type of perturbation to perform. Options are:
”full” : A full perturbation of all terms (default option). “discharge_soft” : Perturb all discharging soft atom charge terms (i.e. value->0.0). “vanish_soft” : Perturb all vanishing soft atom LJ terms (i.e. value->0.0). “flip” : Perturb all hard atom terms as well as bonds/angles. “grow_soft” : Perturb all growing soft atom LJ terms (i.e. 0.0->value). “charge_soft” : Perturb all charging soft atom LJ terms (i.e. 0.0->value).
Currently perturubation_type != “full” is only supported by BioSimSpace.Process.Somd.
Methods
__init__
([lam, lam_vals, min_lam, max_lam, …])Constructor.
Get the value of the perturbation parameter.
Get the index of the lambda value within the lambda array.
Get the list of lambda values.
Get the perturbation type.
Return the pressure.
Return the interval between reporting statistics.
Return the interval between saving restart confiugrations, and/or trajectory frames.
Return the running time.
Return temperature.
Return the time step.
setLambdaValues
(lam[, lam_vals, min_lam, …])Set the list of lambda values.
setPerturbationType
(perturbation_type)Set the perturbation type.
setPressure
(pressure)Set the pressure.
setReportInterval
(report_interval)Set the interval at which statistics are reported.
setRestartInterval
(restart_interval)Set the interval between saving restart confiugrations, and/or trajectory frames.
setRunTime
(runtime)Set the running time.
setTemperature
(temperature)Set the temperature.
setTimeStep
(timestep)Set the time step.
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getLambda
()¶ Get the value of the perturbation parameter.
- Returns
lam – The value of the perturbation parameter.
- Return type
float
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getLambdaIndex
()¶ Get the index of the lambda value within the lambda array.
- Returns
index – The index of the lambda value in teh lambda array.
- Return type
int
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getLambdaValues
()¶ Get the list of lambda values.
- Returns
lam_vals – The list of lambda values.
- Return type
[float]
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getPerturbationType
()¶ Get the perturbation type.
- Returns
perturbation_type – The perturbation type.
- Return type
str
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getReportInterval
()¶ Return the interval between reporting statistics. (In integration steps.).
- Returns
report_interval – The number of integration steps between reporting statistics.
- Return type
int
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getRestartInterval
()¶ Return the interval between saving restart confiugrations, and/or trajectory frames. (In integration steps.).
- Returns
restart_interval – The number of integration steps between saving restart configurations and/or trajectory frames.
- Return type
int
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getTemperature
()¶ Return temperature.
- Returns
temperature – The simulation temperature.
- Return type
-
setLambdaValues
(lam, lam_vals=None, min_lam=None, max_lam=None, num_lam=None)¶ Set the list of lambda values.
- Parameters
lam (float) – The perturbation parameter: [0.0, 1.0]
lam_vals ([float]) – A list of lambda values.
min_lam (float) – The minimum lambda value.
max_lam (float) – The maximum lambda value.
num_lam (int) – The number of lambda values.
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setPerturbationType
(perturbation_type)¶ Set the perturbation type.
- Parameters
perturbation_type (str) –
- The type of perturbation to perform. Options are:
”full” : A full perturbation of all terms (default option). “discharge_soft” : Perturb all discharging soft atom charge terms (i.e. value->0.0). “vanish_soft” : Perturb all vanishing soft atom LJ terms (i.e. value->0.0). “flip” : Perturb all hard atom terms as well as bonds/angles. “grow_soft” : Perturb all growing soft atom LJ terms (i.e. 0.0->value). “charge_soft” : Perturb all charging soft atom LJ terms (i.e. 0.0->value).
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setReportInterval
(report_interval)¶ Set the interval at which statistics are reported. (In integration steps.).
- Parameters
report_interval (int) – The number of integration steps between reporting statistics.
-
setRestartInterval
(restart_interval)¶ Set the interval between saving restart confiugrations, and/or trajectory frames. (In integration steps.).
- Parameters
restart_interval (int) – The number of integration steps between saving restart configurations and/or trajectory frames.
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setTemperature
(temperature)¶ Set the temperature.
- Parameters
temperature (
Temperature
) – The simulation temperature.
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