GromacsTopFile¶
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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.
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__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. -
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:
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