parmed.openmm package

Submodules

• parmed.openmm.parameters module
• parmed.openmm.reporters module
• parmed.openmm.topsystem module
• parmed.openmm.utils module
• parmed.openmm.xmlfile module

Module contents

This is a collection of all of the OpenMM functionality supported in ParmEd

class parmed.openmm.EnergyMinimizerReporter(f, volume=False, **kwargs)

Bases: parmed.openmm.reporters.StateDataReporter

This class acts as a simple energy reporter class for minimizations. This is not meant to be used as a reporter for OpenMM’s molecular dynamics routines, but instead passed a simulation object for printing out single-point energies.

Parameters

fstr or file-like

File name or object to write energies to

volumebool, optional

If True, write the system volume (default is False)

Methods

describeNextReport(*args, **kwargs)	Disable this reporter inside MD
finalize()	Closes any open file
report(simulation[, frame])	Print out the current energy

describeNextReport(*args, **kwargs)

Disable this reporter inside MD

finalize()

Closes any open file

report(simulation, frame=None)

Print out the current energy

class parmed.openmm.MdcrdReporter(**kwargs)

Bases: object

MdcrdReporter prints a trajectory in ASCII Amber format. This reporter will be significantly slower than binary file reporters (like DCDReporter or NetCDFReporter).

Parameters

filestr

Name of the file to write the trajectory to

reportIntervalint

Number of steps between writing trajectory frames

crdsbool=True

Write coordinates to this trajectory file?

velsbool=False

Write velocities to this trajectory file?

frcsbool=False

Write forces to this trajectory file?

Notes

You can only write one of coordinates, forces, or velocities to a mdcrd file.

Methods

describeNextReport(simulation)	Get information about the next report this object will generate.
finalize()	Closes any open file
report(simulation, state)	Generate a report.

describeNextReport(simulation)

Get information about the next report this object will generate.

Parameters

simulationapp.Simulation

The Simulation to generate a report for

Returns

nsteps, pos, vel, frc, eneint, bool, bool, bool, bool

nsteps is the number of steps until the next report pos, vel, frc, and ene are flags indicating whether positions, velocities, forces, and/or energies are needed from the Context

finalize()

Closes any open file

report(simulation, state)

Generate a report.

Parameters:

• simulation (Simulation) The Simulation to generate a report for

• state (State) The current state of the simulation

class parmed.openmm.NetCDFReporter(**kwargs)

Bases: object

NetCDFReporter prints a trajectory in NetCDF format

Methods

describeNextReport(simulation)	Get information about the next report this object will generate.
finalize()	Closes any open file
report(simulation, state)	Generate a report.

describeNextReport(simulation)

Get information about the next report this object will generate.

Parameters

simulationapp.Simulation

The Simulation to generate a report for

Returns

nsteps, pos, vel, frc, eneint, bool, bool, bool, bool

nsteps is the number of steps until the next report pos, vel, frc, and ene are flags indicating whether positions, velocities, forces, and/or energies are needed from the Context

finalize()

Closes any open file

report(simulation, state)

Generate a report.

Parameters

simulationapp.Simulation

The Simulation to generate a report for

statemm.State

The current state of the simulation

class parmed.openmm.OpenMMParameterSet(*filenames)

Bases: parmed.parameters.ParameterSet, parmed.charmm.parameters.CharmmImproperMatchingMixin

Class storing parameters from an OpenMM parameter set

Parameters

filenamesstr, list of str, file-like, or list of file-like; optional

Either the name of a file or a list of filenames from which parameters should be parsed.

See also

parmed.parameters.ParameterSet

Notes

Order is important in the list of files provided. The parameters are loaded in the order they are provided, and any parameters that are specified in multiple places are overwritten (that is, the last occurrence is the parameter type that is used)

Attributes

combining_rule

Methods

condense([do_dihedrals])	This function goes through each of the parameter type dicts and eliminates duplicate types.
from_parameterset(params[, copy, …])	Instantiates an OpenMMParameterSet from another ParameterSet (or subclass).
from_structure(struct[, …])	Extracts known parameters from a Structure instance
id_format(filename)	Identifies the file type as either an Amber-style frcmod or parm.dat file.
match_improper_type(a1, a2, a3, a4)	Matches an improper type based on atom type names
typeify_templates()	Assign atom types to atom names in templates
write(dest[, provenance, write_unused, …])	Write the parameter set to an XML file for use with OpenMM

classmethod from_parameterset(params, copy=False, remediate_residues=True, unique_atom_types=False)

Instantiates an OpenMMParameterSet from another ParameterSet (or subclass). The main thing this feature is responsible for is converting lower-case atom type names into all upper-case and decorating the name to ensure each atom type name is unique.

Parameters

paramsparmed.parameters.ParameterSet

ParameterSet containing the list of parameters to be converted to as OpenMM-compatible parameter set

copybool, optional, default=False

If True, the returned parameter set is a deep copy of params. If False, the returned parameter set is a shallow copy. Default False.

remediate_residuesbool, optional, default=True

If True, will remove non-chemical bonds and drop Residue definitions that are missing parameters

unique_atom_typesbool

If True, a unique OpenMM atom type will be created for every atom of every residue. In this case, the AtomType objects correspond to atom classes rather than atom types (in the OpenMM terminology).

Returns

new_paramsOpenMMParameterSet

OpenMMParameterSet with the same parameters as that defined in the input parameter set

static id_format(filename)

Identifies the file type as either an Amber-style frcmod or parm.dat file.

Parameters

filenamestr

Name of the file to check format for

Returns

is_fmtbool

True if it is an Amber-style parameter file. False otherwise.

write(dest, provenance=None, write_unused=True, separate_ljforce=False, improper_dihedrals_ordering='default', charmm_imp=False, skip_duplicates=True)

Write the parameter set to an XML file for use with OpenMM

Parameters

deststr or file-like

The name of the file or the file-like object (with a write attribute) to which the XML file will be written

provenancedict, optional

If present, the XML file will be tagged with the available fields. Keys of the dictionary become XML etree.Element tags, the values of the dictionary must be instances of any of: - str / unicode (Py2) or str (Py3) - one XML element with this content is written - list - one XML element per each item of the list is written, all these XML elements use the same tag (key in provenance dict) - dict - one of the keys of this dict must be the same as the key of of the provenance dict under which this dict is nested. The value under this key becomes the content of the XML element. Remaining keys and their values are used to construct attributes of the XML element. Note that OrderedDict’s should be used to ensure appropriate order of the XML elements and their attributes. Default is no provenance. Example (unordered): provenance = {‘Reference’ : [‘Nature’, ‘Cell’],

‘Source’ : {‘Source’: ‘leaprc.ff14SB’, sourcePackage : ‘AmberTools’, sourcePackageVersion : ‘15’}, ‘User’ : ‘Mark’}

write_unusedbool

If False: a) residue templates using unavailable atom types will not be written, b) atom types that are not used in any of the residue templates remaining and parameters including those atom types will not be written. A ParameterWarning is issued if any such residues are found in a).

separate_ljforcebool

If True will use a separate LennardJonesForce to create a CostumNonbondedForce to compute L-J interactions. It will set sigma to 1 and epsilon to 0 in the NonbondedForce so that the NonbondedForce only calculates the electrostatic contribution. It should be set to True when converting a CHARMM force field file that doesn’t have pair-specific L-J modifications (NBFIX in CHARMM) so that the ffxml conversion is compatible with the main charmm36.xml file. Note: —- When pair-specific L-J modifications are present (NBFIX in CHARMM), this behavior is always present and this flag is ignored.

improper_dihedrals_orderingstr

The ordering to use when assigning improper torsions in OpenMM. Default is ‘default’, other option is ‘amber’

charmm_imp: bool

If True, will check for existence of IMPR in each residue and patch template, and write out the explicit improper definition without wildcards in the ffxml file.

skip_duplicatesbool

If True: residues which appear identical to an existing residue will not be written. This is usually the best choice. The most common reason for setting skip_duplicates to false is if you have different parametrizations for stereoisomers. Note that since OpenMM’s residue hashing is not aware of chirality, if you wish to use the results in simulations you will need to explicitly provide the template names for affected residues.

Notes

The generated XML file will have the XML tag DateGenerated added to the provenance information set to the current date. Therefore, you should not provide this information in provenance (it will be removed if it is provided).

class parmed.openmm.ProgressReporter(**kwargs)

Bases: parmed.openmm.reporters.StateDataReporter

A class that prints out a progress report of how much MD (or minimization) has been done, how fast the simulation is running, and how much time is left (similar to the mdinfo file in Amber)

Parameters

fstr

The file name of the progress report file (overwritten each time)

reportIntervalint

The step interval between which to write frames

totalStepsint

The total number of steps that will be run in the simulation (used to estimate time remaining)

potentialEnergybool, optional

Whether to print the potential energy (default True)

kineticEnergybool, optional

Whether to print the kinetic energy (default True)

totalEnergybool, optional

Whether to print the total energy (default True)

temperaturebool, optional

Whether to print the system temperature (default True)

volumebool, optional

Whether to print the system volume (default False)

densitybool, optional

Whether to print the system density (default False)

systemMassfloat or unit.Quantity

The mass of the system used when reporting density (useful in instances where masses are set to 0 to constrain their positions)

Notes

In addition to the above, ProgressReporter also accepts arguments for StateDataReporter

Methods

describeNextReport(simulation)	Get information about the next report this object will generate.
finalize()	Closes any open file
report(simulation, state)	Generate a report and predict the time to completion (and current/overall MD performance)

describeNextReport(simulation)

Get information about the next report this object will generate.

Parameters

simulationapp.Simulation

The Simulation to generate a report for

Returns

nsteps, pos, vel, frc, eneint, bool, bool, bool, bool

nsteps is the number of steps until the next report pos, vel, frc, and ene are flags indicating whether positions, velocities, forces, and/or energies are needed from the Context

report(simulation, state)

Generate a report and predict the time to completion (and current/overall MD performance)

class parmed.openmm.RestartReporter(**kwargs)

Bases: object

Use a reporter to handle writing restarts at specified intervals.

Parameters

filestr

Name of the file to write the restart to.

reportIntervalint

Number of steps between writing restart files

write_multiplebool=False

Either write a separate restart each time (appending the step number in the format .# to the file name given above) if True, or overwrite the same file each time if False

netcdfbool=False

Use the Amber NetCDF restart file format

write_velocitiesbool=True

Write velocities to the restart file. You can turn this off for passing in, for instance, a minimized structure.

Methods

describeNextReport(simulation)	Get information about the next report this object will generate.
finalize()	No-op here
report(sim, state)	Generate a report.

describeNextReport(simulation)

Get information about the next report this object will generate.

Parameters

simulationapp.Simulation

The Simulation to generate a report for

Returns

nsteps, pos, vel, frc, eneint, bool, bool, bool, bool

nsteps is the number of steps until the next report pos, vel, frc, and ene are flags indicating whether positions, velocities, forces, and/or energies are needed from the Context

finalize()

No-op here

report(sim, state)

Generate a report.

Parameters

simapp.Simulation

The Simulation to generate a report for

statemm.State

The current state of the simulation

class parmed.openmm.StateDataReporter(**kwargs)

Bases: object

This class acts as a state data reporter for OpenMM simulations, but it is a little more generalized. Notable differences are:

• It allows the units of the output to be specified, with defaults being those used in Amber (e.g., kcal/mol, angstroms^3, etc.)

• It will write to any object containing a ‘write’ method; not just files. This allows, for instance, writing to a GUI window that implements the desired ‘write’ attribute.

Most of this code is copied from the OpenMM StateDataReporter class, with the above-mentioned changes made.

Parameters

fstr or file-like

Destination to write the state data (file name or file object)

reportIntervalint

Number of steps between state data reports

stepbool, optional

Print out the step number (Default True)

timebool, optional

Print out the simulation time (Defaults True)

potentialEnergybool, optional

Print out the potential energy of the structure (Default True)

kineticEnergybool, optional

Print out the kinetic energy of the structure (Default True)

totalEnergybool, optional

Print out the total energy of the system (Default True)

temperaturebool, optional

Print out the temperature of the system (Default True)

volumebool, optional

Print out the volume of the unit cell. If the system is not periodic, the value is meaningless (Default False)

densitybool, optional

Print out the density of the unit cell. If the system is not periodic, the value is meaningless (Default False)

separatorstr, optional

The string to separate data fields (Default ‘,’)

systemMassfloat, optional

If not None, the density will be computed from this mass, since setting a mass to 0 is used to constrain the position of that particle. (Default None)

energyUnitunit, optional

The units to print energies in (default unit.kilocalories_per_mole)

timeUnitunit, optional

The units to print time in (default unit.picoseconds)

volumeUnitunit, optional

The units print volume in (default unit.angstroms**3)

densityUnitunit, optional

The units to print density in (default unit.grams/unit.item/unit.milliliter)

Methods

describeNextReport(simulation)	Get information about the next report this object will generate.
finalize()	Closes any open file
report(simulation, state)	Generate a report.

describeNextReport(simulation)

Get information about the next report this object will generate.

Parameters

simulationapp.Simulation

The simulation to generate a report for

Returns

nsteps, pos, vel, frc, eneint, bool, bool, bool, bool

nsteps is the number of steps until the next report pos, vel, frc, and ene are flags indicating whether positions, velocities, forces, and/or energies are needed from the Context

finalize()

Closes any open file

report(simulation, state)

Generate a report.

Parameters

simulationapp.Simulation

The Simulation to generate a report for

statemm.State

The current state of the simulation

class parmed.openmm.XmlFile

Bases: object

Wrapper for parsing OpenMM-serialized objects. Supports serialized State, System, Integrator, and ForceField objects.

Methods

id_format(filename)	Identifies the file type as an XML file
parse(*args, **kwargs)	Parses XML file and returns deserialized object.

static id_format(filename)

Identifies the file type as an XML file

Parameters

filenamestr

Name of the file to check format for

Returns

is_fmtbool

True if it is an XML format, False otherwise

static parse(*args, **kwargs)

Parses XML file and returns deserialized object. The return value depends on the serialized object, summarized below

• System : returns simtk.openmm.System

• State : returns simtk.openmm.State

• Integrator : returns simtk.openmm.Integrator subclass

• ForceField : returns simtk.openmm.app.ForceField

Parameters

filenamestr or file-like

The file name or file object containing the XML-serialized object

Returns

objSystem, State, Integrator, or ForceField

The deserialized object

Notes

OpenMM requires the entire contents of this file read into memory. As a result, this function may require a significant amount of memory.

parmed.openmm.energy_decomposition(structure, context, nrg=Unit({BaseUnit(base_dim=BaseDimension('amount'), name='mole', symbol='mol'): - 1.0, ScaledUnit(factor=4.184, master=kilojoule, name='kilocalorie', symbol='kcal'): 1.0}))

This computes the energy of every force group in the given structure and computes the energy for each force group for the given Context. Note, the context must have positions already assigned.

Parameters

structureStructure

This should be the Structure object from which the System object in the Context was created

contextmm.Context

The OpenMM context set up for computing forces and energies

nrgenergy unit, optional

The unit to convert all energies into. Default is kcal/mol

Returns

dict {str:float}

A dictionary mapping the name of the force group (taken from the attribute names of the format XXX_FORCE_GROUP in the structure object) with the energy of that group in

parmed.openmm.energy_decomposition_system(structure, system, platform=None, nrg=Unit({BaseUnit(base_dim=BaseDimension('amount'), name='mole', symbol='mol'): - 1.0, ScaledUnit(factor=4.184, master=kilojoule, name='kilocalorie', symbol='kcal'): 1.0}))

This function computes the energy contribution for all of the different force groups.

Parameters

structureStructure

The Structure with the coordinates for this system

systemmm.System

The OpenMM System object to get decomposed energies from

platformstr

The platform to use. Options are None (default), ‘CPU’, ‘Reference’, ‘CUDA’, and ‘OpenCL’. None will pick default OpenMM platform for this installation and computer

nrgenergy unit, optional

The unit to convert all energies into. Default is kcal/mol

Returns

energieslist of tuple

Each entry is a tuple with the name of the force followed by its contribution

parmed.openmm.load_topology(topology, system=None, xyz=None, box=None, condense_atom_types=True)

Creates a parmed.structure.Structure instance from an OpenMM Topology, optionally filling in parameters from a System

Parameters

topologysimtk.openmm.app.Topology

The Topology instance with the list of atoms and bonds for this system

systemsimtk.openmm.System or str, optional

If provided, parameters from this System will be applied to the Structure. If a string is given, it will be interpreted as the file name of an XML-serialized System, and it will be deserialized into a System before used to supply parameters

xyzstr or array of float

Name of a file containing coordinate information or an array of coordinates. If file has unit cell information, it also uses that information unless box (below) is also specified

boxarray of 6 floats

Unit cell dimensions

condense_atom_typesbool, default=True

If True, create unique atom types based on de-duplicating properties. If False, create one atom type for each atom in the system, even if its properties match an existing atom type.

Returns

structStructure

The structure from the provided topology

Raises

OpenMMWarning if parameters are found that cannot be interpreted or

processed by ParmEd

TypeError if there are any mismatches between the provided topology and

system (e.g., they have different numbers of atoms)

IOError if system is a string and it is not an existing file

Notes

Due to its flexibility with CustomForces, it is entirely possible that the functional form of the potential will be unknown to ParmEd. This function will try to use the energy expression to identify supported potential types that are implemented as CustomForce objects. In particular, quadratic improper torsions, when recognized, will be extracted.

Other CustomForces, including the CustomNonbondedForce used to implement NBFIX (off-diagonal L-J modifications) and the 12-6-4 potential, will not be processed and will result in an unknown functional form.

If an OpenMM Atom.id attribute is populated by a non-integer, it will be used to name the corresponding ParmEd AtomType object.