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, thermostat_time_constant=1.0000 ps, report_interval=100, restart_interval=500, restraint=None, force_constant=10 kcal mol-1 Å-2)[source]¶

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, thermostat_time_constant=1.0000 ps, report_interval=100, restart_interval=500, restraint=None, force_constant=10 kcal mol-1 Å-2)[source]¶

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.)
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.
`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.
`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()[source]¶

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()[source]¶

Return the pressure.

Returns:: pressure – The pressure.
Return type:: Pressure

getReportInterval()[source]¶

Return the interval between reporting statistics. (In integration steps.).

Returns:: report_interval – The number of integration steps between reporting statistics.
Return type:: int

getRestartInterval()[source]¶

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()[source]¶

Return the running time.

Returns:: runtime – The simulation run time.
Return type:: Time

getStartTemperature()[source]¶

Return the starting temperature.

Returns:: temperature – The starting temperature.
Return type:: Temperature

getThermostatTimeConstant()[source]¶

Return the time constant for the thermostat.

Returns:: runtime – The time constant for the thermostat.
Return type:: Time

getTimeStep()[source]¶

Return the time step.

Returns:: time – The integration time step.
Return type:: Time

isConstantTemp()[source]¶

Return whether the protocol has a constant temperature.

Returns:: is_const_temp – Whether the temperature is fixed.
Return type:: bool

classmethod restraints()[source]¶

Return a list of the supported restraint keywords.

Returns:: restraints – A list of the supported restraint keywords.
Return type:: [str]

setEndTemperature(temperature)[source]¶

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)[source]¶

Set the pressure.

Parameters:: pressure (str, Pressure) – The pressure.

setReportInterval(report_interval)[source]¶

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)[source]¶

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)[source]¶

Set the running time.

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

setStartTemperature(temperature)[source]¶

Set the starting temperature.

Parameters:: temperature (str, Temperature) – The starting temperature.

setThermostatTimeConstant(thermostat_time_constant)[source]¶

Set the time constant for the thermostat.

Parameters:: thermostat_time_constant (str, Time) – The time constant for the thermostat.

setTimeStep(timestep)[source]¶

Set the time step.

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