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, 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, 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 ([:class:`Time <BioSimSpace.Types.Time>]) – The time schedule for the steering.

  • restraints ([:class`Restraint <BioSimSpace.Metadynamics.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.

  • 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.

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.

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.

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

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

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 (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 (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 (Temperature) – The simulation temperature.

setTimeStep(timestep)

Set the time step.

Parameters

timestep (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).