BioSimSpace._Config.Gromacs#
- class BioSimSpace._Config.Gromacs(system, protocol, property_map={})[source]#
A class for generating configuration files for GROMACS.
Methods
__init__
(system, protocol[, property_map])Constructor.
createConfig
([version, extra_options, ...])Create the list of configuration strings.
hasBox
()Whether the system has a box.
hasWater
()Whether the system is contains water molecules.
Return whether this is a restart simulation.
Return the report interval based on the protocol value.
Return the restart interval based on the protocol value.
steps
()Return the number of integration steps based on the protocol value.
- createConfig(version=None, extra_options={}, extra_lines=[])[source]#
Create the list of configuration strings.
- versionfloat
The GROMACS version.
- extra_optionsdict
A dictionary containing extra options. Overrides the defaults generated by the protocol.
- extra_lines[str]
A list of extra lines to put at the end of the configuration file.
- Returns:
config – The list of AMBER format configuration strings.
- Return type:
[str]
- hasBox()#
Whether the system has a box.
- Returns:
has_box – Whether the system has a simulation box.
- Return type:
bool
- hasWater()#
Whether the system is contains water molecules.
- Returns:
has_water – Whether the system contains water molecules.
- Return type:
bool
- isRestart()#
Return whether this is a restart simulation.
- Returns:
is_restart – Whether this is a restart simulation.
- Return type:
bool
- reportInterval()#
Return the report interval based on the protocol value.
- Returns:
report_interval – The report interval in integration steps.
- Return type:
int
- restartInterval()#
Return the restart interval based on the protocol value.
- Returns:
restart_interval – The restart interval in integration steps.
- Return type:
int
- steps()#
Return the number of integration steps based on the protocol value.
- Returns:
steps – The number of integration steps.
- Return type:
int