# 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. Return the final temperature. Return the force constant for the restraint. Return the pressure. Return the interval between reporting statistics. Return the interval between saving restart confiugrations, and/or trajectory frames. Return the type of restraint. Return the running time. Return the starting temperature. Return the time step. Return whether the protocol has a constant temperature. 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

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

Return type

class: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.