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, ensemble='NPT')

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, ensemble='NPT')

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.
  • ensemble (str) – The thermodynamic ensemble.

Methods

__init__([lam, lam_vals, min_lam, max_lam, …]) Constructor.
getEnsemble() Return the thermodynamic ensemble.
getLambda() Get the value of the perturbation parameter.
getLambdaValues() Get the list of lambda values.
getRunTime() Return the running time.
getTemperature() Return temperature.
getTimeStep() Return the time step.
setEnsemble(ensemble) Set the thermodynamic ensemble.
setLambdaValues(lam[, lam_vals, min_lam, …]) Set the list of lambda values.
setRunTime(runtime) Set the running time.
setTemperature(temperature) Set the temperature.
setTimeStep(timestep) Set the time step.
getEnsemble()

Return the thermodynamic ensemble.

Returns:ensemble – The thermodynamic ensemble.
Return type:str
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]
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
setEnsemble(ensemble)

Set the thermodynamic ensemble.

Parameters:ensemble (str) – The thermodynamic ensemble.
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.
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.