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, frames=20, 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, frames=20, 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.

  • frames (int) – The number of trajectory frames to record.

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

Methods

__init__([timestep, runtime, …])

Constructor.

getEndTemperature()

Return the final temperature.

getFrames()

Return the number of frames.

getPressure()

Return the pressure.

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.

setFrames(frames)

Set the number of frames.

setPressure(pressure)

Set the pressure.

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

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

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.

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.

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.