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.