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, report_interval=1000, restart_interval=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, report_interval=1000, restart_interval=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.

  • 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.)

  • 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

__init__(collective_variable[, timestep, …])

Constructor.

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.

getReportInterval()

Return the interval between reporting statistics.

getRestartInterval()

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

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.

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.

setRunTime(runtime)

Set the running time.

setTemperature(temperature)

Set the temperature.

setTimeStep(timestep)

Set the time step.

getBiasFactor()

Return the bias factor for well tempered metadynamics.

Returns

bias_factor – The bias factor for well tempered metadynamics.

Return type

float

getCollectiveVariable()

Return the collective variable (or variables).

Returns

collective_variable – The collective variable (or variables) for the simulation.

Return type

[CollectiveVariable]

getColvarFile()

Return the path to the COLVAR file.

Returns

colvar_file – The path to the COLVAR file.

Return type

str

getGridFile()

Return the path to the GRID file.

Returns

grid_file – The path to the GRID file.

Return type

str

getHillFrequency()

Return the frequency at which Gaussian hills are deposited.

Returns

hill_frequency – The frequency at which hills are deposited.

Return type

int

getHillHeight()

Return the height of the Gaussian hills.

Returns

hill_width – The height of the Gaussian hills.

Return type

Energy

getHillsFile()

Return the path to the HILLS file.

Returns

hills_file – The path to the HILLS file.

Return type

str

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

getTemperature()

Return temperature.

Returns

temperature – The simulation temperature.

Return type

Temperature

getTimeStep()

Return the time step.

Returns

timestep – The integration time step.

Return type

Time

setBiasFactor(bias_factor=None)

Set the bias factor for well tempered metadynamics. Call with no arguments to clear the bias factor.

Parameters

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

setCollectiveVariable(collective_variable)

Set the collective variable (or variables).

Parameters

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

setColvarFile(colvar_file)

Set the location of an existing COLVAR file.

Parameters

colvar_file (str) – The path to an existing COLVAR file.

setGridFile(grid_file)

Set the location of an existing GRID file.

Parameters

grid_file (str) – The path to an existing GRID file.

setHillFrequency(hill_frequency)

Set the frequency at which Gaussian hills are deposited.

Parameters

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

setHillHeight(hill_height)

Set the height of the Gaussian hills.

Parameters

hill_height (Energy) – The hill height.

setHillsFile(hills_file)

Set the location of an existing HILLS file.

Parameters

hills_file (str) – The path to an existing HILLS file.

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.

setRunTime(runtime)

Set the running time.

Parameters

runtime (Time) – The simulation run time.

setTemperature(temperature)

Set the temperature.

Parameters

temperature (Temperature) – The simulation temperature.

setTimeStep(timestep)

Set the time step.

Parameters

timestep (Time) – The integration time step.