BioSimSpace.Protocol.Equilibration

class BioSimSpace.Protocol.Equilibration(timestep=2.0000 fs, runtime=1.0000 ns, temperature_start=300.0000 K, temperature_end=300.0000 K, temperature=None, pressure=None, thermostat_time_constant=1.0000 ps, report_interval=200, restart_interval=1000, restart=False, restraint=None, force_constant=10 kcal mol-1 Å-2)

A class for storing equilibration protocols.

__init__(timestep=2.0000 fs, runtime=1.0000 ns, temperature_start=300.0000 K, temperature_end=300.0000 K, temperature=None, pressure=None, thermostat_time_constant=1.0000 ps, report_interval=200, restart_interval=1000, restart=False, restraint=None, force_constant=10 kcal mol-1 Å-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.

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

• 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.)

• restart (bool) – Whether this is a continuation of a previous simulation.

• 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.
getThermostatTimeConstant()	Return the time constant for the thermostat.
getTimeStep()	Return the time step.
isConstantTemp()	Return whether the protocol has a constant temperature.
isRestart()	Return whether this restart simulation.
restraints()	Return a list of the supported restraint keywords.
setEndTemperature(temperature)	Set the final temperature.
setForceConstant(force_constant)	Set the force constant for the restraint.
setPressure(pressure)	Set the pressure.
setReportInterval(report_interval)	Set the interval at which statistics are reported.
setRestart(restart)	Set the restart flag.
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.
setThermostatTimeConstant(...)	Set the time constant for the thermostat.
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:

float, str, 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, 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

getStartTemperature()

Return the starting temperature.

Returns:

temperature – The starting 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:

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

isRestart()

Return whether this restart simulation.

Returns:

is_restart – Whether this is a restart simulation.

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 (str, Temperature) – The final temperature.

setForceConstant(force_constant)

Set the force constant for the restraint.

Parameters:

force_constant (int, float, str, GeneralUnit, float) – The force constant for the restraint, in units of kcal_per_mol/angstrom**2.

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.

setRestart(restart)

Set the restart flag.

Parameters:

restart (bool) – Whether this is a restart simulation.

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 (str, Time) – The simulation run time.

setStartTemperature(temperature)

Set the starting temperature.

Parameters:

temperature (str, Temperature) – The starting 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:

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