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, frames=20, ensemble='NVT', 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, frames=20, ensemble='NVT', restrain_backbone=False)

Constructor.

Parameters:
  • timestep (Time) – The integration timestep (in femtoseconds).
  • runtime (Time) – The running time (in nanoseconds).
  • temperature_start (Temperature) – The starting temperature (in Kelvin).
  • temperature_end (Temperature) – The final temperature (in Kelvin).
  • temperature (Temperature) – The equilibration temperature (in Kelvin). This takes precedence of over the other temperatures, i.e. to run at fixed temperature.
  • frames (int) – The number of trajectory frames to record.
  • ensemble (str) – The thermodynamic ensemble.
  • restrain_backbone (bool) – Whether the atoms in the backbone are fixed.

Methods

__init__([timestep, runtime, …]) Constructor.
getEndTemperature() Return the final temperature.
getEnsemble() Return the thermodynamic ensemble.
getFrames() Return the number of 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.
setEnsemble(ensemble) Set the thermodynamic ensemble.
setFrames(frames) Set the number of 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
getEnsemble()

Return the thermodynamic ensemble.

Returns:ensemble – The thermodynamic ensemble.
Return type:str
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
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.
setEnsemble(ensemble)

Set the thermodynamic ensemble.

Parameters:ensemble (str) – The thermodynamic ensemble.
setFrames(frames)

Set the number of frames.

Parameters:frames (int) – The number of 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.