BioSimSpace.Protocol.Steering

class BioSimSpace.Protocol.Steering(collective_variable, schedule, restraints, verse='both', timestep=2.0000 fs, runtime=1.0000 ns, temperature=300.0000 K, pressure=1.0000 atm, thermostat_time_constant=1.0000 ps, report_interval=1000, restart_interval=1000, colvar_file=None)

A class for storing steered molecular dynamics protocols.

__init__(collective_variable, schedule, restraints, verse='both', timestep=2.0000 fs, runtime=1.0000 ns, temperature=300.0000 K, pressure=1.0000 atm, thermostat_time_constant=1.0000 ps, report_interval=1000, restart_interval=1000, colvar_file=None)

Constructor.

Parameters:

• collective_variable (CollectiveVariable, [CollectiveVariable]) – The collective variable (or variables) used to perform the steering.

• schedule ([Time]) – The time schedule for the steering.

• restraints ([Restraint] [(Restraint)]]) – The position of the restraint on each collective variable for each stage of the schedule.

• verse (str) – Whether the restraint is acting for values of the collective variable “larger” or “smaller” than the restraint, or acting on “both” sides (default).

• 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.

• restart_interval (int) – The frequency at which restart configurations and trajectory frames are saved. (In integration steps.)

• 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, schedule, ...)	Constructor.
getCollectiveVariable()	Return the collective variable (or variables).
getColvarFile()	Return the path to the COLVAR file.
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.
getRestraints()	Return the restraint on each collective variable for each stage in the schedule.
getRunTime()	Return the running time.
getSchedule()	Return steering schedule.
getTemperature()	Return temperature.
getThermostatTimeConstant()	Return the time constant for the thermostat.
getTimeStep()	Return the time step.
getVerse()	Returns whether the restraint is acting for values of the collective variable "larger" or "smaller" than the restraint, or acting on "both" sides (default).
setCollectiveVariable(collective_variable)	Set the collective variable (or variables).
setColvarFile(colvar_file)	Set the location of an existing COLVAR 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.
setRestraints(restraints)	Set the restraints for the steering schedule.
setRunTime(runtime)	Set the running time.
setSchedule(schedule)	Set the steering schedule.
setTemperature(temperature)	Set the temperature.
setThermostatTimeConstant(...)	Set the time constant for the thermostat.
setTimeStep(timestep)	Set the time step.
setVerse(verse)	Set whether the restraint is acting for values of the collective variable "larger" or "smaller" than the restraint, or acting on "both" sides (default).

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

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]

getRestraints()

Return the restraint on each collective variable for each stage in the schedule.

Returns:

restraints – The position of the restraint on each collective variable for each stage of the schedule.

Return type:

[:class`CollectiveVariable <BioSimSpace.Metadynamics.CollectiveVariable>`] [(CollectiveVariable)]]

getRunTime()

Return the running time.

Returns:

runtime – The simulation run time.

Return type:

Time

getSchedule()

Return steering schedule.

Returns:

schedule – The schedule for the steering, i.e. the integration time steps at which restraints are applied/adjusted.

Return type:

[int]

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

getVerse()

Returns whether the restraint is acting for values of the collective variable “larger” or “smaller” than the restraint, or acting on “both” sides (default).

Returns:

verse – Whether the restraint is acting for values of the collective variable “larger” or “smaller” than the restraint, or acting on “both” sides (default).

Return type:

str

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.

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.

setRestraints(restraints)

Set the restraints for the steering schedule.

Parameters:

restraint ([:class`Restraint <BioSimSpace.Metadynamics.Restraint>`] [(Restraint)]]) – The position of the restraint on each collective variable for each stage of the schedule.

setRunTime(runtime)

Set the running time.

Parameters:

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

setSchedule(schedule)

Set the steering schedule.

Parameters:

schedule ([Time]) – The time schedule for the steering.

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.

setVerse(verse)

Set whether the restraint is acting for values of the collective variable “larger” or “smaller” than the restraint, or acting on “both” sides (default).

Parameters:

verse (str, [str]) – Whether the restraint is acting for values of the collective variable “larger” or “smaller” than the restraint, or acting on “both” sides (default).