BioSimSpace.Process.Gromacs

class BioSimSpace.Process.Gromacs(system, protocol, exe=None, name='gromacs', work_dir=None, seed=None, property_map={})

A class for running simulations using GROMACS.

__init__(system, protocol, exe=None, name='gromacs', work_dir=None, seed=None, property_map={})

Constructor.

Parameters
  • system (System) – The molecular system.

  • protocol (Protocol) – The protocol for the GROMACS process.

  • exe (str) – The full path to the GROMACS executable.

  • name (str) – The name of the process.

  • work_dir – The working directory for the process.

  • seed (int) – A random number seed.

  • property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }

Methods

__delattr__

Implement delattr(self, name).

__dir__

Default dir() implementation.

__eq__

Return self==value.

__format__

Default object formatter.

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(system, protocol[, exe, name, …])

Constructor.

__init_subclass__

This method is called when a class is subclassed.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__

Create and return a new object.

__reduce__

Helper for pickle.

__reduce_ex__

Helper for pickle.

__repr__()

Return a string showing how to instantiate the object.

__setattr__

Implement setattr(self, name, value).

__sizeof__

Size of object in memory, in bytes.

__str__()

Return a human readable string representation of the object.

__subclasshook__

Abstract classes can override this to customize issubclass().

_clear_output()

Reset stdout and stderr.

_find_trajectory_file()

Helper function to find the trajectory file associated with the process.

_generate_args()

Generate the dictionary of command-line arguments.

_generate_binary_run_file()

Use grommp to generate the binary run input file.

_generate_config()

Generate GROMACS configuration file strings.

_getCollectiveVariable(index[, time_series, …])

Get the value of a collective variable.

_getFrame(time)

Get the trajectory frame closest to a specific time value.

_getFreeEnergy([index, stride, kt, block])

Get the current free energy estimate.

_getPlumedConfig()

Return the list of PLUMED configuration strings.

_getPlumedConfigFile()

Return path to the PLUMED config file.

_getTime([time_series, block])

Get the time (in nanoseconds).

_get_stdout_record(key[, time_series, unit])

Helper function to get a stdout record from the dictionary.

_sampleConfigurations(bounds[, number, block])

Sample configurations based on values of the collective variable(s).

_setPlumedConfig(config)

Set the list of PLUMED configuration file strings.

_setup()

Setup the input files and working directory ready for simulation.

_update_stdout_dict()

Update the dictonary of thermodynamic records.

_writePlumedConfig(file)

Write the PLUMED configuration to file.

addArgs(args)

Append additional command-line arguments.

addToConfig(config)

Add a string to the configuration list.

clearArgs()

Clear all of the command-line arguments.

command()

Return the command-line string used to run the process.

deleteArg(arg)

Delete an argument from the dictionary.

exe()

Return the executable.

getAngleEnergy([time_series, block])

Get the angle energy.

getArgString()

Get the command-line arguments string.

getArgStringList()

Convert the argument dictionary into a list of strings.

getArgs()

Get the dictionary of command-line arguments.

getBondEnergy([time_series, block])

Get the bond energy.

getConfig()

Get the list of configuration file strings.

getConservedEnergy([time_series, block])

Get the conserved energy.

getConstraintRMSD([time_series, block])

Get the RMSD of the constrained atoms.

getCoulomb14([time_series, block])

Get the Coulomb energy between atoms 1 and 4.

getCoulombReciprocal([time_series, block])

Get the reciprocal space Coulomb energy.

getCoulombSR([time_series, block])

Get the short-range Coulomb energy.

getCurrentAngleEnergy([time_series])

Get the current angle energy.

getCurrentBondEnergy([time_series])

Get the current bond energy.

getCurrentConservedEnergy([time_series])

Get the current conserved energy.

getCurrentConstraintRMSD([time_series])

Get the current RMSD of the constrained atoms.

getCurrentCoulomb14([time_series])

Get the current Coulomb energy between atoms 1 and 4.

getCurrentCoulombReciprocal([time_series])

Get the current reciprocal space Coulomb energy.

getCurrentCoulombSR([time_series])

Get the current short-range Coulomb energy.

getCurrentDihedralEnergy([time_series])

Get the current dihedral energy.

getCurrentDispersionCorrection([time_series])

Get the current dispersion correction.

getCurrentImproperEnergy([time_series])

Get the current improper energy.

getCurrentKineticEnergy([time_series])

Get the current kinetic energy.

getCurrentLennardJones14([time_series])

Get the current Lennard-Jones energy between atoms 1 and 4.

getCurrentLennardJonesSR([time_series])

Get the current short-range Lennard-Jones energy.

getCurrentPotentialEnergy([time_series])

Get the current potential energy.

getCurrentPressure([time_series])

Get the current pressure.

getCurrentPressureDC([time_series])

Get the current DC pressure.

getCurrentRecord(record[, time_series, unit])

Get a current record from the stdout dictionary.

getCurrentRecords()

Return the current dictionary of stdout time-series records.

getCurrentRestraintEnergy([time_series])

Get the current position restraint energy.

getCurrentStep([time_series])

Get the current number of integration steps.

getCurrentSystem()

Get the latest molecular system.

getCurrentTemperature([time_series])

Get the current temperature.

getCurrentTime([time_series])

Get the current time (in nanoseconds).

getCurrentTotalEnergy([time_series])

Get the current total energy.

getDihedralEnergy([time_series, block])

Get the dihedral energy.

getDispersionCorrection([time_series, block])

Get the dispersion correction.

getImproperEnergy([time_series, block])

Get the improper energy.

getInput([name, file_link])

Return a link to a zip file containing the input files used by the process.

getKinetecEnergy([time_series, block])

Get the kinetic energy.

getLennardJones14([time_series, block])

Get the Lennard-Jones energy between atoms 1 and 4.

getLennardJonesSR([time_series, block])

Get the short-range Lennard-Jones energy.

getName()

Return the process name.

getOutput([name, block, file_link])

Return a link to a zip file of the working directory.

getPackageName()

Return the package name.

getPotentialEnergy([time_series, block])

Get the potential energy.

getPressure([time_series, block])

Get the pressure.

getPressureDC([time_series, block])

Get the DC pressure.

getRecord(record[, time_series, unit, block])

Get a record from the stdout dictionary.

getRecords([block])

Return the dictionary of stdout time-series records.

getRestraintEnergy([time_series, block])

Get the position restraint energy.

getSeed()

Return the random number seed.

getStderr([block])

Return the entire stderr for the process as a list of strings.

getStdout([block])

Return the entire stdout for the process as a list of strings.

getStep([time_series, block])

Get the number of integration steps.

getSystem([block])

Get the latest molecular system.

getTemperature([time_series, block])

Get the temperature.

getTime([time_series, block])

Get the time (in nanoseconds).

getTotalEnergy([time_series, block])

Get the total energy.

getTrajectory([block])

Return a trajectory object.

inputFiles()

Return the list of input files.

insertArg(arg, value, index)

Insert a command-line argument at a specific index.

isError()

Return whether the process errored.

isQueued()

Return whether the process is queued.

isRunning()

Return whether the process is running.

kill()

Kill the running process.

resetArgs()

Reset the command-line arguments.

resetConfig()

Reset the configuration parameters.

run([system, protocol, auto_start, restart])

Create and run a new process.

runTime()

Return the running time for the process (in minutes).

setArg(arg, value)

Set a specific command-line argument.

setArgs(args)

Set the dictionary of command-line arguments.

setConfig(config)

Set the list of configuration file strings.

setName(name)

Set the process name.

setSeed(seed)

Set the random number seed.

start()

Start the GROMACS process.

stderr([n])

Print the last n lines of the stderr buffer.

stdout([n])

Print the last n lines of the stdout buffer.

wait([max_time])

Wait for the process to finish.

workDir()

Return the working directory.

writeConfig(file)

Write the configuration to file.

Attributes

__dict__

__doc__

__module__

__weakref__

list of weak references to the object (if defined)