BioSimSpace.Protocol.Equilibration¶
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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.
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__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.
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getEndTemperature()¶ Return the final temperature.
- Returns
temperature – The final temperature.
- Return type
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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
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getReportInterval()¶ Return the interval between reporting statistics. (In integration steps.).
- Returns
report_interval – The number of integration steps between reporting statistics.
- Return type
int
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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
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getRestraint()¶ Return the type of restraint.
- Returns
restraint – The type of restraint.
- Return type
str, [int]
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getStartTemperature()¶ Return the starting temperature.
- Returns
temperature – The starting temperature.
- Return type
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isConstantTemp()¶ Return whether the protocol has a constant temperature.
- Returns
is_const_temp – Whether the temperature is fixed.
- Return type
bool
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classmethod
restraints()¶ Return a list of the supported restraint keywords.
- Returns
restraints – A list of the supported restraint keywords.
- Return type
[str]
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setEndTemperature(temperature)¶ Set the final temperature.
- Parameters
temperature (
Temperature) – The final temperature.
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setForceConstant(force_constant)¶ Set the type force constant for the restraint.
- Parameters
force_constant (
GeneralUnit, float) –
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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.
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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.
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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.
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setStartTemperature(temperature)¶ Set the starting temperature.
- Parameters
temperature (
Temperature) – The starting temperature.
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