BioSimSpace.Protocol.Production

class BioSimSpace.Protocol.Production(timestep=2.0000 fs, runtime=1.0000 ns, temperature=300.0000 K, frames=20, ensemble='NPT', first_step=0, restart=False)

A class for storing production protocols.

__init__(timestep=2.0000 fs, runtime=1.0000 ns, temperature=300.0000 K, frames=20, ensemble='NPT', first_step=0, restart=False)

Constructor.

Parameters:
  • timestep (Time) – The integration timestep.
  • runtime (Time) – The running time.
  • temperature (Temperature) – The temperature.
  • frames (int) – The number of trajectory frames to record.
  • ensemble (str) – The thermodynamic ensemble.
  • first_step (int) – The initial time step (for restart simulations).
  • restart (bool) – Whether this is a continuation of a previous simulation.

Methods

__init__([timestep, runtime, temperature, …]) Constructor.
getEnsemble() Return the thermodynamic ensemble.
getFirstStep() Return the first time step.
getFrames() Return the number of frames.
getRunTime() Return the running time.
getTemperature() Return temperature.
getTimeStep() Return the time step.
isRestart() Return whether this restart simulation.
setEnsemble(ensemble) Set the thermodynamic ensemble.
setFirstStep(first_step) Set the initial time step.
setFrames(frames) Set the number of frames.
setRestart(restart) Set the restart flag.
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
getFirstStep()

Return the first time step.

Returns:step – The first time step.
Return type:int
getFrames()

Return the number of frames.

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

Return whether this restart simulation.

Returns:is_restart – Whether this is a restart simulation.
Return type:bool
setEnsemble(ensemble)

Set the thermodynamic ensemble.

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

Set the initial time step.

Parameters:step (int) – The first time step.
setFrames(frames)

Set the number of frames.

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

Set the restart flag.

Parameters:restart (bool) – Whether this is a restart simulation.
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.