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

__delattr__(name, /)

Implement delattr(self, name).

__dir__()

Default dir() implementation.

__eq__(value, /)

Return self==value.

__format__(format_spec, /)

Default object formatter.

__ge__(value, /)

Return self>=value.

__getattribute__(name, /)

Return getattr(self, name).

__gt__(value, /)

Return self>value.

__hash__()

Return hash(self).

__init__([timestep, runtime, …])

Constructor.

__init_subclass__

This method is called when a class is subclassed.

__le__(value, /)

Return self<=value.

__lt__(value, /)

Return self<value.

__ne__(value, /)

Return self!=value.

__new__(**kwargs)

Create and return a new object.

__reduce__()

Helper for pickle.

__reduce_ex__(protocol, /)

Helper for pickle.

__repr__()

Return a string showing how to instantiate the object.

__setattr__(name, value, /)

Implement setattr(self, name, value).

__sizeof__()

Size of object in memory, in bytes.

__str__()

Return a human readable string representation of the object.

__subclasshook__

Abstract classes can override this to customize issubclass().

_setCustomised(is_customised)

Internal function to flag whether a protocol has been customised.

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.

Attributes

__dict__

__doc__

__module__

__weakref__

list of weak references to the object (if defined)