GromacsTopFile

class simtk.openmm.app.gromacstopfile.GromacsTopFile(file, periodicBoxVectors=None, unitCellDimensions=None, includeDir=None, defines=None)

GromacsTopFile parses a Gromacs top file and constructs a Topology and (optionally) an OpenMM System from it.

__init__(file, periodicBoxVectors=None, unitCellDimensions=None, includeDir=None, defines=None)

Load a top file.

Parameters:
  • file (str) – the name of the file to load
  • periodicBoxVectors (tuple of Vec3=None) – the vectors defining the periodic box
  • unitCellDimensions (Vec3=None) – the dimensions of the crystallographic unit cell. For non-rectangular unit cells, specify periodicBoxVectors instead.
  • includeDir (string=None) – A directory in which to look for other files included from the top file. If not specified, we will attempt to locate a gromacs installation on your system. When gromacs is installed in /usr/local, this will resolve to /usr/local/gromacs/share/gromacs/top
  • defines (dict={}) – preprocessor definitions that should be predefined when parsing the file

Methods

__init__(file[, periodicBoxVectors, ...]) Load a top file.
createSystem([nonbondedMethod, ...]) Construct an OpenMM System representing the topology described by this prmtop file.
__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__
__setattr__

x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int

size of object in memory, in bytes

__str__
createSystem(nonbondedMethod=NoCutoff, nonbondedCutoff=Quantity(value=1.0, unit=nanometer), constraints=None, rigidWater=True, implicitSolvent=None, soluteDielectric=1.0, solventDielectric=78.5, ewaldErrorTolerance=0.0005, removeCMMotion=True, hydrogenMass=None)

Construct an OpenMM System representing the topology described by this prmtop file.

Parameters:
  • nonbondedMethod (object=NoCutoff) – The method to use for nonbonded interactions. Allowed values are NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
  • nonbondedCutoff (distance=1*nanometer) – The cutoff distance to use for nonbonded interactions
  • constraints (object=None) – Specifies which bonds and angles should be implemented with constraints. Allowed values are None, HBonds, AllBonds, or HAngles.
  • rigidWater (boolean=True) – If true, water molecules will be fully rigid regardless of the value passed for the constraints argument
  • implicitSolvent (object=None) – If not None, the implicit solvent model to use. The only allowed value is OBC2.
  • soluteDielectric (float=1.0) – The solute dielectric constant to use in the implicit solvent model.
  • solventDielectric (float=78.5) – The solvent dielectric constant to use in the implicit solvent model.
  • ewaldErrorTolerance (float=0.0005) – The error tolerance to use if nonbondedMethod is Ewald or PME.
  • removeCMMotion (boolean=True) – If true, a CMMotionRemover will be added to the System
  • hydrogenMass (mass=None) – The mass to use for hydrogen atoms bound to heavy atoms. Any mass added to a hydrogen is subtracted from the heavy atom to keep their total mass the same.
Returns:

the newly created System
Return type:

System