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)[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, report_interval=100, restart_interval=500, restraint=None, force_constant=10.0000 M Q-1 T-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.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()[source]#
Return the final temperature.
- Returns:
temperature – The final temperature.
- Return type:
- getForceConstant()[source]#
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
- 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()[source]#
Return the type of restraint.
- Returns:
restraint – The type of restraint.
- Return type:
str, [int]
- getRunTime()[source]#
Return the running time.
- Returns:
runtime – The simulation run time.
- Return type:
- getStartTemperature()[source]#
Return the starting temperature.
- Returns:
temperature – The starting temperature.
- Return type:
- getTimeStep()[source]#
Return the time step.
- Returns:
time – The integration time step.
- Return type:
- 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 (
Temperature
) – The final temperature.
- setForceConstant(force_constant)[source]#
Set the type force constant for the restraint.
- Parameters:
force_constant (
GeneralUnit
, float) –
- 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)[source]#
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 (
Time
) – The simulation run time.
- setStartTemperature(temperature)[source]#
Set the starting temperature.
- Parameters:
temperature (
Temperature
) – The starting temperature.