AmoebaTorsionTorsionForce¶
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class
simtk.openmm.openmm.
AmoebaTorsionTorsionForce
(*args)¶ This class implements the Amoeba torsion-torsion interaction.
To use it, create an AmoebaTorsionTorsionForce object then call addTorsionTorsion() once for each torsion-torsion. After a torsion-torsion has been added, you can modify its force field parameters by calling setTorsionTorsionParameters().
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__init__
(self) → AmoebaTorsionTorsionForce¶ __init__(self, other) -> AmoebaTorsionTorsionForce
Create an AmoebaTorsionTorsionForce.
Methods
__init__
((self) -> AmoebaTorsionTorsionForce)__init__(self, other) -> AmoebaTorsionTorsionForce addTorsionTorsion
((self, particle1, ...)Add a torsion-torsion term to the force field. getForceGroup
((self) -> int)Get the force group this Force belongs to. getNumTorsionTorsionGrids
((self) -> int)Get the number of torsion-torsion grids getNumTorsionTorsions
((self) -> int)Get the number of torsion-torsion terms in the potential function getTorsionTorsionGrid
((self, index) -> vectorddd)Get the torsion-torsion grid at the specified index getTorsionTorsionParameters
(self, index)Get the force field parameters for a torsion-torsion term. setForceGroup
(self, group)Set the force group this Force belongs to. setTorsionTorsionGrid
(self, index, grid)Set the torsion-torsion grid at the specified index setTorsionTorsionParameters
(self, index, ...)Set the force field parameters for a torsion-torsion term. setUsesPeriodicBoundaryConditions
(self, periodic)Set whether this force should apply periodic boundary conditions when calculating displacements. usesPeriodicBoundaryConditions
((self) -> bool)Returns whether or not this force makes use of periodic boundary conditions. -
__copy__
(self) → Force¶
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getForceGroup
(self) → int¶ Get the force group this Force belongs to.
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setForceGroup
(self, group)¶ Set the force group this Force belongs to.
Parameters: group (int) – the group index. Legal values are between 0 and 31 (inclusive).
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getNumTorsionTorsions
(self) → int¶ Get the number of torsion-torsion terms in the potential function
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getNumTorsionTorsionGrids
(self) → int¶ Get the number of torsion-torsion grids
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addTorsionTorsion
(self, particle1, particle2, particle3, particle4, particle5, chiralCheckAtomIndex, gridIndex) → int¶ Add a torsion-torsion term to the force field.
Parameters: - particle1 (int) – the index of the first particle connected by the torsion-torsion
- particle2 (int) – the index of the second particle connected by the torsion-torsion
- particle3 (int) – the index of the third particle connected by the torsion-torsion
- particle4 (int) – the index of the fourth particle connected by the torsion-torsion
- particle5 (int) – the index of the fifth particle connected by the torsion-torsion
- chiralCheckAtomIndex (int) – the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
- gridIndex (int) – the index to the grid to be used
Returns: the index of the torsion-torsion that was added
Return type: int
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getTorsionTorsionParameters
(self, index)¶ Get the force field parameters for a torsion-torsion term.
Parameters: index (int) – the index of the torsion-torsion for which to get parameters Returns: - particle1 (int) – the index of the first particle connected by the torsion-torsion
- particle2 (int) – the index of the second particle connected by the torsion-torsion
- particle3 (int) – the index of the third particle connected by the torsion-torsion
- particle4 (int) – the index of the fourth particle connected by the torsion-torsion
- particle5 (int) – the index of the fifth particle connected by the torsion-torsion
- chiralCheckAtomIndex (int) – the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
- gridIndex (int) – the grid index
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setTorsionTorsionParameters
(self, index, particle1, particle2, particle3, particle4, particle5, chiralCheckAtomIndex, gridIndex)¶ Set the force field parameters for a torsion-torsion term.
Parameters: - index (int) – the index of the torsion-torsion for which to set parameters
- particle1 (int) – the index of the first particle connected by the torsion-torsion
- particle2 (int) – the index of the second particle connected by the torsion-torsion
- particle3 (int) – the index of the third particle connected by the torsion-torsion
- particle4 (int) – the index of the fourth particle connected by the torsion-torsion
- particle5 (int) – the index of the fifth particle connected by the torsion-torsion
- chiralCheckAtomIndex (int) – the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
- gridIndex (int) – the grid index
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getTorsionTorsionGrid
(self, index) → vectorddd¶ Get the torsion-torsion grid at the specified index
Parameters: index (int) – the grid index Returns: vector< std – grid return grid reference Return type: :vector< std::vector< double > > >
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setTorsionTorsionGrid
(self, index, grid)¶ Set the torsion-torsion grid at the specified index
Parameters: - index (int) – the index of the torsion-torsion for which to get parameters
- grid (vector< std::vector< std::vector< double > > >) – either 3 or 6 values may be specified per grid point. If the derivatives are omitted, they are calculated automatically by fitting a 2D spline to the energies. grid[x][y][0] = x value grid[x][y][1] = y value grid[x][y][2] = energy grid[x][y][3] = dEdx value grid[x][y][4] = dEdy value grid[x][y][5] = dEd(xy) value
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setUsesPeriodicBoundaryConditions
(self, periodic)¶ Set whether this force should apply periodic boundary conditions when calculating displacements. Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
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usesPeriodicBoundaryConditions
(self) → bool¶ Returns whether or not this force makes use of periodic boundary conditions.
Returns: true if force uses PBC and false otherwise Return type: bool
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