BioSimSpace.Protocol.Equilibration

class BioSimSpace.Protocol.Equilibration(timestep=2.0000 fs, runtime=0.2000 ns, temperature_start=300.0000 K, temperature_end=300.0000 K, temperature=None, pressure=None, report_interval=100, restart_interval=500, restrain_backbone=False)

A class for storing equilibration protocols.

__init__(timestep=2.0000 fs, runtime=0.2000 ns, temperature_start=300.0000 K, temperature_end=300.0000 K, temperature=None, pressure=None, report_interval=100, restart_interval=500, restrain_backbone=False)

Constructor.

Parameters
  • timestep (Time) – The integration timestep.

  • runtime (Time) – The running time.

  • temperature_start (Temperature) – The starting temperature.

  • temperature_end (Temperature) – The final temperature.

  • temperature (Temperature) – The equilibration temperature. This takes precedence of over the other temperatures, i.e. to run at fixed temperature.

  • pressure (Pressure) – The pressure. If this argument is omitted then the simulation is run using the NVT ensemble.

  • report_interval (int) – The frequency at which statistics are recorded. (In integration steps.)

  • restart_interval (int) – The frequency at which restart configurations and trajectory frames are saved. (In integration steps.)

  • restrain_backbone (bool) – Whether the atoms in the backbone are fixed.

Methods

__init__([timestep, runtime, …])

Constructor.

getEndTemperature()

Return the final temperature.

getPressure()

Return the pressure.

getReportInterval()

Return the interval between reporting statistics.

getRestartInterval()

Return the interval between saving restart confiugrations, and/or trajectory frames.

getRunTime()

Return the running time.

getStartTemperature()

Return the starting temperature.

getTimeStep()

Return the time step.

isConstantTemp()

Return whether the protocol has a constant temperature.

isRestrained()

Return whether the backbone is restrained.

setEndTemperature(temperature)

Set the final temperature.

setPressure(pressure)

Set the pressure.

setReportInterval(report_interval)

Set the interval at which statistics are reported.

setRestartInterval(restart_interval)

Set the interval between saving restart confiugrations, and/or trajectory frames.

setRestraint(restrain_backbone)

Set the backbone restraint.

setRunTime(runtime)

Set the running time.

setStartTemperature(temperature)

Set the starting temperature.

setTimeStep(timestep)

Set the time step.

getEndTemperature()

Return the final temperature.

Returns

temperature – The final temperature.

Return type

Temperature

getPressure()

Return the pressure.

Returns

pressure – The pressure.

Return type

Pressure

getReportInterval()

Return the interval between reporting statistics. (In integration steps.)

Returns

report_interval – The number of integration steps between reporting statistics.

Return type

int

getRestartInterval()

Return the interval between saving restart confiugrations, and/or trajectory frames. (In integration steps.)

Returns

restart_interval – The number of integration steps between saving restart configurations and/or trajectory frames.

Return type

int

getRunTime()

Return the running time.

Returns

runtime – The simulation run time.

Return type

Time

getStartTemperature()

Return the starting temperature.

Returns

temperature – The starting temperature.

Return type

Temperature

getTimeStep()

Return the time step.

Returns

time – The integration time step.

Return type

Time

isConstantTemp()

Return whether the protocol has a constant temperature.

Returns

is_const_temp – Whether the temperature is fixed.

Return type

bool

isRestrained()

Return whether the backbone is restrained.

Returns

is_restrained – Whether the backbone is restrained.

Return type

bool

setEndTemperature(temperature)

Set the final temperature.

Parameters

temperature (Temperature) – The final temperature.

setPressure(pressure)

Set the pressure.

Parameters

pressure (Pressure) – The pressure.

setReportInterval(report_interval)

Set the interval at which statistics are reported. (In integration steps.)

Parameters

report_interval (int) – The number of integration steps between reporting statistics.

setRestartInterval(restart_interval)

Set the interval between saving restart confiugrations, and/or trajectory frames. (In integration steps.)

Parameters

restart_interval (int) – The number of integration steps between saving restart configurations and/or trajectory frames.

setRestraint(restrain_backbone)

Set the backbone restraint.

Parameters

is_restrained (bool) – Whether the backbone is restrained.

setRunTime(runtime)

Set the running time.

Parameters

runtime (Time) – The simulation run time.

setStartTemperature(temperature)

Set the starting temperature.

Parameters

temperature (Temperature) – The starting temperature.

setTimeStep(timestep)

Set the time step.

Parameters

time (Time) – The integration time step.