BioSimSpace.Process.Gromacs¶

class BioSimSpace.Process.Gromacs(system, protocol, exe=None, name='gromacs', work_dir=None, seed=None, property_map={}, ignore_warnings=False, show_errors=True, checkpoint_file=None)¶

A class for running simulations using GROMACS.

__init__(system, protocol, exe=None, name='gromacs', work_dir=None, seed=None, property_map={}, ignore_warnings=False, show_errors=True, checkpoint_file=None)¶

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” }
ignore_warnings (bool) – Whether to ignore warnings when generating the binary run file with ‘gmx grompp’. By default, these warnings are elevated to errors and will halt the program.
show_errors (bool) – Whether to show warning/error messages when generating the binary run file.
checkpoint_file (str) – The path to a checkpoint file from a previous run. This can be used to continue an existing simulation. Currently we only support the use of checkpoint files for Equilibration protocols.

Methods

`__init__`(system, protocol[, exe, name, …])	Constructor.
`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 total dihedral energy (proper + improper).
`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.
`getCurrentProperEnergy`([time_series])	Get the current proper dihedral energy.
`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 simulation time.
`getCurrentTotalEnergy`([time_series])	Get the current total energy.
`getDihedralEnergy`([time_series, block])	Get the total dihedral energy (proper + improper).
`getDispersionCorrection`([time_series, block])	Get the dispersion correction.
`getFrame`(index)	Return a specific trajectory frame.
`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.
`getKineticEnergy`([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.
`getProperEnergy`([time_series, block])	Get the proper dihedral energy.
`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 simulation time.
`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 exited with an error.
`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.

addArgs(args)¶

Append additional command-line arguments.

Parameters: args (dict, collections.OrderedDict) – A dictionary of command line arguments.

addToConfig(config)¶

Add a string to the configuration list.

Parameters: config (str, [str]) – A configuration string, a list of configuration strings, or a path to a configuration file.

clearArgs()¶: Clear all of the command-line arguments.

command()¶

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

Returns: command – The command string.
Return type: str

deleteArg(arg)¶

Delete an argument from the dictionary.

Parameters: arg (str) – The argument to delete.

exe()¶

Return the executable.

Returns: exe – The path to the executable.
Return type: str

getAngleEnergy(time_series=False, block='AUTO')¶

Get the angle energy.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

energy – The angle energy.

Return type

Energy

getArgString()¶

Get the command-line arguments string.

Returns: arg_string – The command-line argument string.
Return type: str

getArgStringList()¶

Convert the argument dictionary into a list of strings.

Returns: arg_string_list – The list of command-line arguments.
Return type: [str]

getArgs()¶

Get the dictionary of command-line arguments.

Returns: args – The dictionary of command-line arguments.
Return type: collections.OrderedDict

getBondEnergy(time_series=False, block='AUTO')¶

Get the bond energy.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

energy – The bond energy.

Return type

Energy

getConfig()¶

Get the list of configuration file strings.

Returns: config – The list of configuration strings.
Return type: [str]

getConservedEnergy(time_series=False, block='AUTO')¶

Get the conserved energy.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

energy – The conserved energy.

Return type

Energy

getConstraintRMSD(time_series=False, block='AUTO')¶

Get the RMSD of the constrained atoms.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

length – The constrained RMSD.

Return type

Length

getCoulomb14(time_series=False, block='AUTO')¶

Get the Coulomb energy between atoms 1 and 4.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

energy – The Coulomb energy.

Return type

Energy

getCoulombReciprocal(time_series=False, block='AUTO')¶

Get the reciprocal space Coulomb energy.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

energy – The Coulomb energy.

Return type

Energy

getCoulombSR(time_series=False, block='AUTO')¶

Get the short-range Coulomb energy.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

energy – The Coulomb energy.

Return type

Energy

getCurrentAngleEnergy(time_series=False)¶

Get the current angle energy.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: energy – The angle energy.
Return type: Energy

getCurrentBondEnergy(time_series=False)¶

Get the current bond energy.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: energy – The bond energy.
Return type: Energy

getCurrentConservedEnergy(time_series=False)¶

Get the current conserved energy.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: energy – The conserved energy.
Return type: Energy

getCurrentConstraintRMSD(time_series=False)¶

Get the current RMSD of the constrained atoms.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: length – The current constrained RMSD.
Return type: Length

getCurrentCoulomb14(time_series=False)¶

Get the current Coulomb energy between atoms 1 and 4.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: energy – The Coulomb energy.
Return type: Energy

getCurrentCoulombReciprocal(time_series=False)¶

Get the current reciprocal space Coulomb energy.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: energy – The Coulomb energy.
Return type: Energy

getCurrentCoulombSR(time_series=False)¶

Get the current short-range Coulomb energy.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: energy – The Coulomb energy.
Return type: Energy

getCurrentDihedralEnergy(time_series=False)¶

Get the current total dihedral energy (proper + improper).

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: energy – The dihedral energy.
Return type: Energy

getCurrentDispersionCorrection(time_series=False)¶

Get the current dispersion correction.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: energy – The dispersion correction.
Return type: Energy

getCurrentImproperEnergy(time_series=False)¶

Get the current improper energy.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: energy – The improper energy.
Return type: Energy

getCurrentKineticEnergy(time_series=False)¶

Get the current kinetic energy.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: energy – The kinetic energy.
Return type: Energy

getCurrentLennardJones14(time_series=False)¶

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

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: energy – The Lennard-Jones energy.
Return type: Energy

getCurrentLennardJonesSR(time_series=False)¶

Get the current short-range Lennard-Jones energy.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: energy – The Lennard-Jones energy.
Return type: Energy

getCurrentPotentialEnergy(time_series=False)¶

Get the current potential energy.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: energy – The potential energy.
Return type: Energy

getCurrentPressure(time_series=False)¶

Get the current pressure.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: pressure – The current pressure.
Return type: Pressure

getCurrentPressureDC(time_series=False)¶

Get the current DC pressure.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: pressure – The current pressure.
Return type: Pressure

getCurrentProperEnergy(time_series=False)¶

Get the current proper dihedral energy.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: energy – The proper dihedral energy.
Return type: Energy

getCurrentRecord(record, time_series=False, unit=None)¶

Get a current record from the stdout dictionary.

Parameters

record (str) – The record key.
time_series (bool) – Whether to return a list of time series records.
unit (Unit) – The unit to convert the record to.

Returns

record – The matching record.

Return type

Type

getCurrentRecords()¶

Return the current dictionary of stdout time-series records.

Parameters: block (bool) – Whether to block until the process has finished running.
Returns: records – The dictionary of time-series records.
Return type: MultiDict

getCurrentRestraintEnergy(time_series=False)¶

Get the current position restraint energy.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: energy – The dispersion correction.
Return type: Energy

getCurrentStep(time_series=False)¶

Get the current number of integration steps.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: step – The current number of integration steps.
Return type: int

getCurrentSystem()¶

Get the latest molecular system.

Returns: system – The latest molecular system.
Return type: System

getCurrentTemperature(time_series=False)¶

Get the current temperature.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: temperature – The current temperature.
Return type: Temperature

getCurrentTime(time_series=False)¶

Get the current simulation time.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

time – The current simulation time in nanoseconds.

Return type

Time

getCurrentTotalEnergy(time_series=False)¶

Get the current total energy.

Parameters: time_series (bool) – Whether to return a list of time series records.
Returns: energy – The total energy.
Return type: Energy

getDihedralEnergy(time_series=False, block='AUTO')¶

Get the total dihedral energy (proper + improper).

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

energy – The total dihedral energy.

Return type

Energy

getDispersionCorrection(time_series=False, block='AUTO')¶

Get the dispersion correction.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

energy – The dispersion correction.

Return type

Energy

getFrame(index)¶

Return a specific trajectory frame.

Parameters: index (int) – The index of the frame.
Returns: frame – The System object of the corresponding frame.
Return type: System

getImproperEnergy(time_series=False, block='AUTO')¶

Get the improper energy.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

energy – The improper energy.

Return type

Energy

getInput(name=None, file_link=False)¶

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

Parameters

name (str) – The name of the zip file.
file_link (bool) – Whether to return a FileLink when working in Jupyter.

Returns

output – A path, or file link, to an archive of the process input.

Return type

str, IPython.display.FileLink

getKineticEnergy(time_series=False, block='AUTO')¶

Get the kinetic energy.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

energy – The kinetic energy.

Return type

Energy

getLennardJones14(time_series=False, block='AUTO')¶

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

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

energy – The Lennard-Jones energy.

Return type

Energy

getLennardJonesSR(time_series=False, block='AUTO')¶

Get the short-range Lennard-Jones energy.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

energy – The short-range Lennard-Jones energy.

Return type

Energy

getName()¶

Return the process name.

Returns:

namestr: The name of the process.

getOutput(name=None, block='AUTO', file_link=False)¶

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

Parameters

name (str) – The name of the zip file.
block (bool) – Whether to block until the process has finished running.
file_link (bool) – Whether to return a FileLink when working in Jupyter.

Returns

output – A path, or file link, to an archive of the process output.

Return type

str, IPython.display.FileLink

getPackageName()¶

Return the package name.

Returns: name – The name of the package.
Return type: str

getPotentialEnergy(time_series=False, block='AUTO')¶

Get the potential energy.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

energy – The potential energy.

Return type

Energy

getPressure(time_series=False, block='AUTO')¶

Get the pressure.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

pressure – The pressure.

Return type

Pressure

getPressureDC(time_series=False, block='AUTO')¶

Get the DC pressure.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

pressure – The DC pressure.

Return type

Pressure

getProperEnergy(time_series=False, block='AUTO')¶

Get the proper dihedral energy.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

energy – The proper dihedral energy.

Return type

Energy

getRecord(record, time_series=False, unit=None, block='AUTO')¶

Get a record from the stdout dictionary.

Parameters

record (str) – The record key.
time_series (bool) – Whether to return a list of time series records.
unit (Unit) – The unit to convert the record to.
block (bool) – Whether to block until the process has finished running.

Returns

record – The matching record.

Return type

Type

getRecords(block='AUTO')¶

Return the dictionary of stdout time-series records.

Parameters: block (bool) – Whether to block until the process has finished running.
Returns: records – The dictionary of time-series records.
Return type: MultiDict

getRestraintEnergy(time_series=False, block='AUTO')¶

Get the position restraint energy.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

energy – The dispersion correction.

Return type

Energy

getSeed()¶

Return the random number seed.

Returns: seed – The random number seed.
Return type: int

getStderr(block='AUTO')¶

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

Parameters: block (bool) – Whether to block until the process has finished running.
Returns: error – The list of stderror strings.
Return type: [str]

getStdout(block='AUTO')¶

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

Parameters: block (bool) – Whether to block until the process has finished running.
Returns: output – The list of stdout strings.
Return type: [str]

getStep(time_series=False, block='AUTO')¶

Get the number of integration steps.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

step – The current number of integration steps.

Return type

int

getSystem(block='AUTO')¶

Get the latest molecular system.

Parameters: block (bool) – Whether to block until the process has finished running.
Returns: system – The latest molecular system.
Return type: System

getTemperature(time_series=False, block='AUTO')¶

Get the temperature.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

temperature – The temperature.

Return type

Temperature

getTime(time_series=False, block='AUTO')¶

Get the simulation time.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

time – The current simulation time in nanoseconds.

Return type

Time

getTotalEnergy(time_series=False, block='AUTO')¶

Get the total energy.

Parameters

time_series (bool) – Whether to return a list of time series records.
block (bool) – Whether to block until the process has finished running.

Returns

energy – The total energy.

Return type

Energy

getTrajectory(block='AUTO')¶

Return a trajectory object.

Parameters: block (bool) – Whether to block until the process has finished running.
Returns: trajectory – The latest trajectory object.
Return type: System

inputFiles()¶

Return the list of input files.

Returns: input_files – The list of autogenerated input files.
Return type: [str]

insertArg(arg, value, index)¶

Insert a command-line argument at a specific index.

Parameters

arg (str) – The argument to set.
value – The value of the argument.
index (int) – The index in the dictionary.

isError()¶

Return whether the process exited with an error.

Returns: is_error – Whether the process exited with an error.
Return type: bool

isQueued()¶

Return whether the process is queued.

Returns: is_queued – Whether the process is queued.
Return type: bool

isRunning()¶

Return whether the process is running.

Returns: is_running – Whether the process is running.
Return type: bool

kill()¶: Kill the running process.

resetArgs()¶: Reset the command-line arguments.

resetConfig()¶: Reset the configuration parameters.

run(system=None, protocol=None, auto_start=True, restart=False)¶

Create and run a new process.

Parameters

system (System) – The molecular system.
protocol (Protocol) – The simulation protocol.
auto_start (bool) – Whether to start the process automatically.
restart (bool) – Whether to restart the simulation, i.e. use the original system.

Returns

process – The new process object.

Return type

Procees

runTime()¶

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

Returns: runtime – The runtime in minutes.
Return type: Time

setArg(arg, value)¶

Set a specific command-line argument.

For command-line flags, i.e. boolean arguments, the key should specify whether the flag is enabled (True) or not (False).

Parameters

arg (str) – The argument to set.
value (bool, str) – The value of the argument.

setArgs(args)¶

Set the dictionary of command-line arguments.

Parameters: args (dict, collections.OrderedDict) – A dictionary of command-line arguments.

setConfig(config)¶

Set the list of configuration file strings.

Parameters: config (str, [str]) – The list of configuration strings, or a path to a configuration file.

setName(name)¶

Set the process name.

Parameters: name (str) – The process name.

setSeed(seed)¶

Set the random number seed.

Parameters: seed (int) – The random number seed.

start()¶

Start the GROMACS process.

Returns: process – A handle to the GROMACS process.
Return type: Process.Gromacs

stderr(n=10)¶

Print the last n lines of the stderr buffer.

Parameters: n (int) – The number of lines to print.

stdout(n=10)¶

Print the last n lines of the stdout buffer.

Parameters: n (int) – The number of lines to print.

wait(max_time=None)¶

Wait for the process to finish.

Parameters: max_time (Time, int, float) – The maximum time to wait (in minutes).

workDir()¶

Return the working directory.

Returns: work_dir – The path of the working directory.
Return type: str

writeConfig(file)¶

Write the configuration to file.

Parameters: file (str) – The path to a file.