BioSimSpace.Protocol.Equilibration

class BioSimSpace.Protocol.Equilibration(timestep=2.0000 fs, runtime=0.2000 ns, temperature_start=300.0000 K, temperature_end=300.0000 K, temperature=None, pressure=None, report_interval=100, restart_interval=500, restraint=None, force_constant=10.0000 M Q-1 T-2)

A class for storing equilibration protocols.

__init__(timestep=2.0000 fs, runtime=0.2000 ns, temperature_start=300.0000 K, temperature_end=300.0000 K, temperature=None, pressure=None, report_interval=100, restart_interval=500, restraint=None, force_constant=10.0000 M Q-1 T-2)

Constructor.

Parameters
  • timestep (Time) – The integration timestep.

  • runtime (Time) – The running time.

  • temperature_start (Temperature) – The starting temperature.

  • temperature_end (Temperature) – The final temperature.

  • temperature (Temperature) – The equilibration temperature. This takes precedence of over the other temperatures, i.e. to run at fixed temperature.

  • pressure (Pressure) – The pressure. If this argument is omitted then the simulation is run using the NVT ensemble.

  • 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.)

  • restraint (str, [int]) –

    The type of restraint to perform. This should be one of the following options:

    ”backbone”

    Protein backbone atoms. The matching is done by a name template, so is unreliable on conversion between molecular file formats.

    ”heavy”

    All non-hydrogen atoms that aren’t part of water molecules or free ions.

    ”all”

    All atoms that aren’t part of water molecules or free ions.

    Alternatively, the user can pass a list of atom indices for more fine-grained control. If None, then no restraints are used.

  • force_constant (GeneralUnit, float) – The force constant for the restraint potential. If a ‘float’ is passed, then default units of ‘kcal_per_mol / angstrom**2’ will be used.

Methods

__init__([timestep, runtime, …])

Constructor.

getEndTemperature()

Return the final temperature.

getForceConstant()

Return the force constant for the restraint.

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.

getStartTemperature()

Return the starting temperature.

getTimeStep()

Return the time step.

isConstantTemp()

Return whether the protocol has a constant temperature.

restraints()

Return a list of the supported restraint keywords.

setEndTemperature(temperature)

Set the final temperature.

setForceConstant(force_constant)

Set the type force constant for the restraint.

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.

setRestraint(restraint)

Set the type of restraint.

setRunTime(runtime)

Set the running time.

setStartTemperature(temperature)

Set the starting temperature.

setTimeStep(timestep)

Set the time step.

getEndTemperature()

Return the final temperature.

Returns

temperature – The final temperature.

Return type

Temperature

getForceConstant()

Return the force constant for the restraint.

Returns

The force constant for the restraint, in units of kcal_per_mol/angstrom**2.

Return type

force_constant GeneralUnit

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.

Return type

str, [int]

getRunTime()

Return the running time.

Returns

runtime – The simulation run time.

Return type

Time

getStartTemperature()

Return the starting temperature.

Returns

temperature – The starting temperature.

Return type

Temperature

getTimeStep()

Return the time step.

Returns

time – The integration time step.

Return type

Time

isConstantTemp()

Return whether the protocol has a constant temperature.

Returns

is_const_temp – Whether the temperature is fixed.

Return type

bool

classmethod restraints()

Return a list of the supported restraint keywords.

Returns

restraints – A list of the supported restraint keywords.

Return type

[str]

setEndTemperature(temperature)

Set the final temperature.

Parameters

temperature (Temperature) – The final temperature.

setForceConstant(force_constant)

Set the type force constant for the restraint.

Parameters

force_constant (GeneralUnit, float) –

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.

setRestraint(restraint)

Set the type of restraint.

Parameters

restraint (str, [int]) –

The type of restraint to perform. This should be one of the following options:

”backbone”

Protein backbone atoms. The matching is done by a name template, so is unreliable on conversion between molecular file formats.

”heavy”

All non-hydrogen atoms that aren’t part of water molecules or free ions.

”all”

All atoms that aren’t part of water molecules or free ions.

Alternatively, the user can pass a list of atom indices for more fine-grained control.

setRunTime(runtime)

Set the running time.

Parameters

runtime (Time) – The simulation run time.

setStartTemperature(temperature)

Set the starting temperature.

Parameters

temperature (Temperature) – The starting temperature.

setTimeStep(timestep)

Set the time step.

Parameters

time (Time) – The integration time step.