BioSimSpace.Protocol.FreeEnergy¶

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.

__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.
`getFrames`()	Return the number of frames.
`getLambda`()	Get the value of the perturbation parameter.
`getLambdaValues`()	Get the list of lambda values.
`getPressure`()	Return the pressure.
`getRunTime`()	Return the running time.
`getTemperature`()	Return temperature.
`getTimeStep`()	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.

getFrames()¶

Return the number of frames.

Returns: frames – The number of trajectory frames.
Return type: int

getLambda()¶

Get the value of the perturbation parameter.

Returns: lam – The value of the perturbation parameter.
Return type: float

getLambdaValues()¶

Get the list of lambda values.

Returns: lam_vals – The list of lambda values.
Return type: [float]

getPressure()¶

Return the pressure.

Returns: pressure – The pressure.
Return type: Pressure

getRunTime()¶

Return the running time.

Returns: runtime – The simulation run time.
Return type: Time

getTemperature()¶

Return temperature.

Returns: temperature – The simulation temperature.
Return type: Temperature

getTimeStep()¶

Return the time step.

Returns: timestep – The integration time step.
Return type: Time

setFrames(frames)¶

Set the number of frames.

Parameters: frames (int) – The number of trajectory frames.

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.

setPressure(pressure)¶

Set the pressure.

Parameters: pressure (Pressure) – The pressure.

setRunTime(runtime)¶

Set the running time.

Parameters: runtime (Time) – The simulation run time.

setTemperature(temperature)¶

Set the temperature.

Parameters: temperature (Temperature) – The simulation temperature.

setTimeStep(timestep)¶

Set the time step.

Parameters: timestep (Time) – The integration time step.