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)¶

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)¶

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.

Methods

`__init__`(collective_variable[, timestep, …])	Constructor.
`getBiasFactor`()	Return the bias factor for well tempered metadynamics.
`getCollectiveVariable`()	Return the collective variable (or variables).
`getHillFrequency`()	Return the frequency at which Gaussian hills are deposited.
`getHillHeight`()	Return the height of the Gaussian hills.
`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).
`setHillFrequency`(hill_frequency)	Set the frequency at which Gaussian hills are deposited.
`setHillHeight`(hill_height)	Set the height of the Gaussian hills.
`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]

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

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.

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.

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.