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, thermostat_time_constant=1.0000 ps, 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, thermostat_time_constant=1.0000 ps, 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.

• thermostat_time_constant (Time) – Time constant for thermostat coupling.

• 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.
getRestraint()	Return the type of restraint.
getRunTime()	Return the running time.
getTemperature()	Return temperature.
getThermostatTimeConstant()	Return the time constant for the thermostat.
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.
setThermostatTimeConstant(...)	Set the time constant for the thermostat.
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

getRestraint()

Return the type of restraint.

Returns:

restraint – The type of restraint, either a keyword or a list of atom indices.

Return type:

str, [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

getThermostatTimeConstant()

Return the time constant for the thermostat.

Returns:

runtime – The time constant for the thermostat.

Return type:

Time

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 (str, Energy) – The hill height.

setPressure(pressure)

Set the pressure.

Parameters:

pressure (str, 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 (str, Time) – The simulation run time.

setTemperature(temperature)

Set the temperature.

Parameters:

temperature (str, Temperature) – The simulation temperature.

setThermostatTimeConstant(thermostat_time_constant)

Set the time constant for the thermostat.

Parameters:

thermostat_time_constant (str, Time) – The time constant for the thermostat.

setTimeStep(timestep)

Set the time step.

Parameters:

timestep (str, Time) – The integration time step.