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=1.0000 ns, temperature=300.0000 K, pressure=1.0000 atm, frames=20)¶ 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=1.0000 ns, temperature=300.0000 K, pressure=1.0000 atm, frames=20)¶ 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.frames (int) – The number of trajectory frames to record.
Methods
__init__
([lam, lam_vals, min_lam, max_lam, …])Constructor.
Return the number of frames.
Get the value of the perturbation parameter.
Get the list of lambda values.
Return the pressure.
Return the running time.
Return temperature.
Return the time step.
setFrames
(frames)Set the number of frames.
setLambdaValues
(lam[, lam_vals, min_lam, …])Set the list of lambda values.
setPressure
(pressure)Set the pressure.
setRunTime
(runtime)Set the running time.
setTemperature
(temperature)Set the temperature.
setTimeStep
(timestep)Set the time step.
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getFrames
()¶ Return the number of frames.
- Returns
frames – The number of trajectory frames.
- Return type
int
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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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getLambdaValues
()¶ Get the list of lambda values.
- Returns
lam_vals – The list of lambda values.
- Return type
[float]
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getTemperature
()¶ Return temperature.
- Returns
temperature – The simulation temperature.
- Return type
-
setFrames
(frames)¶ Set the number of frames.
- Parameters
frames (int) – The number of trajectory frames.
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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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setTemperature
(temperature)¶ Set the temperature.
- Parameters
temperature (
Temperature
) – The simulation temperature.
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