AmoebaTorsionTorsionForce¶
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class
OpenMM::
AmoebaTorsionTorsionForce
¶ This class implements the Amoeba torsion-torsion interaction.
To use it, create an
AmoebaTorsionTorsionForce()
object then calladdTorsionTorsion()
once for each torsion-torsion. After a torsion-torsion has been added, you can modify its force field parameters by callingsetTorsionTorsionParameters()
.Methods
AmoebaTorsionTorsionForce()
Create an AmoebaTorsionTorsionForce()
.getNumTorsionTorsions()
Get the number of torsion-torsion terms in the potential function getNumTorsionTorsionGrids()
Get the number of torsion-torsion grids addTorsionTorsion()
Add a torsion-torsion term to the force field. getTorsionTorsionParameters()
Get the force field parameters for a torsion-torsion term. setTorsionTorsionParameters()
Set the force field parameters for a torsion-torsion term. getTorsionTorsionGrid()
Get the torsion-torsion grid at the specified index setTorsionTorsionGrid()
Set the torsion-torsion grid at the specified index usesPeriodicBoundaryConditions()
Returns whether or not this force makes use of periodic boundary conditions. -
AmoebaTorsionTorsionForce
(void)¶ Create an
AmoebaTorsionTorsionForce()
.
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int
getNumTorsionTorsions
(void) const¶ Get the number of torsion-torsion terms in the potential function
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int
getNumTorsionTorsionGrids
(void) const¶ Get the number of torsion-torsion grids
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int
addTorsionTorsion
(int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex)¶ Add a torsion-torsion term to the force field.
Parameters: - particle1 – the index of the first particle connected by the torsion-torsion
- particle2 – the index of the second particle connected by the torsion-torsion
- particle3 – the index of the third particle connected by the torsion-torsion
- particle4 – the index of the fourth particle connected by the torsion-torsion
- particle5 – the index of the fifth particle connected by the torsion-torsion
- chiralCheckAtomIndex – the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
- gridIndex – the index to the grid to be used
Returns: the index of the torsion-torsion that was added
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void
getTorsionTorsionParameters
(int index, int &particle1, int &particle2, int &particle3, int &particle4, int &particle5, int &chiralCheckAtomIndex, int &gridIndex) const¶ Get the force field parameters for a torsion-torsion term.
Parameters: - index – the index of the torsion-torsion for which to get parameters
- particle1 – [out] the index of the first particle connected by the torsion-torsion
- particle2 – [out] the index of the second particle connected by the torsion-torsion
- particle3 – [out] the index of the third particle connected by the torsion-torsion
- particle4 – [out] the index of the fourth particle connected by the torsion-torsion
- particle5 – [out] the index of the fifth particle connected by the torsion-torsion
- chiralCheckAtomIndex – [out] the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
- gridIndex – [out] the grid index
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void
setTorsionTorsionParameters
(int index, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex)¶ Set the force field parameters for a torsion-torsion term.
Parameters: - index – the index of the torsion-torsion for which to set parameters
- particle1 – the index of the first particle connected by the torsion-torsion
- particle2 – the index of the second particle connected by the torsion-torsion
- particle3 – the index of the third particle connected by the torsion-torsion
- particle4 – the index of the fourth particle connected by the torsion-torsion
- particle5 – the index of the fifth particle connected by the torsion-torsion
- chiralCheckAtomIndex – the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
- gridIndex – the grid index
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const std::vector<std::vector<std::vector<double>>> &
getTorsionTorsionGrid
(int index) const¶ Get the torsion-torsion grid at the specified index
Parameters: - index – the grid index
Returns: grid return grid reference
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void
setTorsionTorsionGrid
(int index, const std::vector<std::vector<std::vector<double>>> &grid)¶ Set the torsion-torsion grid at the specified index
Parameters: - index – the index of the torsion-torsion for which to get parameters
- grid – 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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bool
usesPeriodicBoundaryConditions
() const¶ Returns whether or not this force makes use of periodic boundary conditions.
Returns: true if nonbondedMethod uses PBC and false otherwise
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