BioSimSpace.Protocol.Metadynamics

class BioSimSpace.Protocol.Metadynamics(collective_variable, timestep=2.0000 fs, runtime=1.0000 ns, temperature=300.0000 K, pressure=1.0000 atm, hill_height=1.0000 kJ/mol, hill_frequency=1000, bias_factor=None, hills_file=None, grid_file=None, colvar_file=None)

A class for storing metadynamics protocols.

__init__(collective_variable, timestep=2.0000 fs, runtime=1.0000 ns, temperature=300.0000 K, pressure=1.0000 atm, hill_height=1.0000 kJ/mol, hill_frequency=1000, bias_factor=None, hills_file=None, grid_file=None, colvar_file=None)

Constructor.

Parameters
  • collective_variable (CollectiveVariable, [CollectiveVariable]) – The collective variable (or variables) for the simulation.

  • 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.

  • hill_height (Energy) – The height of the Gaussian hills.

  • hill_frequency (int) – The frequency at which hills are deposited.

  • bias_factor (float) – The bias factor for well tempered metadynamics.

  • hills_file (str) – The path to a HILLS file from a previous simulation. This can be used to restart in order to contiune sampling. The information in the file must be consistent with the ‘collective_variable’ argument.

  • grid_file (str) – The path to a GRID file from a previous simulation. This can be used to restart in order to continue sampling. The information in the file must be consistent with the ‘collective_variable’ argument.

  • colvar_file (str) – The path to a COLVAR file from a previous simulation. The information in the file must be consistent with the ‘collective_variable’ argument.

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__(collective_variable[, timestep, …])

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.

getBiasFactor()

Return the bias factor for well tempered metadynamics.

getCollectiveVariable()

Return the collective variable (or variables).

getColvarFile()

Return the path to the COLVAR file.

getGridFile()

Return the path to the GRID file.

getHillFrequency()

Return the frequency at which Gaussian hills are deposited.

getHillHeight()

Return the height of the Gaussian hills.

getHillsFile()

Return the path to the HILLS file.

getPressure()

Return the pressure.

getRunTime()

Return the running time.

getTemperature()

Return temperature.

getTimeStep()

Return the time step.

setBiasFactor([bias_factor])

Set the bias factor for well tempered metadynamics.

setCollectiveVariable(collective_variable)

Set the collective variable (or variables).

setColvarFile(colvar_file)

Set the location of an existing COLVAR file.

setGridFile(grid_file)

Set the location of an existing GRID file.

setHillFrequency(hill_frequency)

Set the frequency at which Gaussian hills are deposited.

setHillHeight(hill_height)

Set the height of the Gaussian hills.

setHillsFile(hills_file)

Set the location of an existing HILLS file.

setPressure(pressure)

Set the pressure.

setRunTime(runtime)

Set the running time.

setTemperature(temperature)

Set the temperature.

setTimeStep(timestep)

Set the time step.

Attributes

__dict__

__doc__

__module__

__weakref__

list of weak references to the object (if defined)