GromacsTopFile parses a Gromacs top file and constructs a Topology and (optionally) an OpenMM System from it.
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def | __init__ |
| Load a top file.
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def | createSystem |
| Construct an OpenMM System representing the topology described by this prmtop file.
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| topology |
| The Topology read from the prmtop file.
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GromacsTopFile parses a Gromacs top file and constructs a Topology and (optionally) an OpenMM System from it.
def __init__ |
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self, |
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file, |
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unitCellDimensions = None , |
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includeDir = '/usr/local/gromacs/share/gromacs/top' , |
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defines = {} |
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) |
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Load a top file.
- Parameters
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file | (string) the name of the file to load |
unitCellDimensions | (Vec3=None) the dimensions of the crystallographic unit cell |
includeDir | (string=/usr/local/gromacs/share/gromacs/top) a directory in which to look for other files included from the top file |
defines | (map={}) preprocessor definitions that should be predefined when parsing the file |
def createSystem |
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self, |
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nonbondedMethod = ff.NoCutoff , |
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nonbondedCutoff = 1.0*unit.nanometer , |
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constraints = None , |
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rigidWater = True , |
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implicitSolvent = None , |
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soluteDielectric = 1.0 , |
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solventDielectric = 78.5 , |
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ewaldErrorTolerance = 0.0005 , |
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removeCMMotion = True |
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) |
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Construct an OpenMM System representing the topology described by this prmtop file.
- Parameters
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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 |
- Returns
- the newly created System
The Topology read from the prmtop file.
The documentation for this class was generated from the following file: