BioSimSpace.Protocol.Production

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

A class for storing production protocols.

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

Constructor.

Parameters
  • 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.

  • 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.

getFirstStep()

Return the first time step.

getFrames()

Return the number of frames.

getPressure()

Return the pressure.

getRunTime()

Return the running time.

getTemperature()

Return temperature.

getTimeStep()

Return the time step.

isRestart()

Return whether this restart simulation.

setFirstStep(first_step)

Set the initial time step.

setFrames(frames)

Set the number of frames.

setPressure(pressure)

Set the pressure.

setRestart(restart)

Set the restart flag.

setRunTime(runtime)

Set the running time.

setTemperature(temperature)

Set the temperature.

setTimeStep(timestep)

Set the time step.

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

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

isRestart()

Return whether this restart simulation.

Returns

is_restart – Whether this is a restart simulation.

Return type

bool

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.

setPressure(pressure)

Set the pressure.

Parameters

pressure (Pressure) – The pressure.

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.