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
Create an
AmoebaTorsionTorsionForce
.Get the number of torsion-torsion terms in the potential function
Get the number of torsion-torsion grids
Add a torsion-torsion term to the force field.
Get the force field parameters for a torsion-torsion term.
Set the force field parameters for a torsion-torsion term.
Get the torsion-torsion grid at the specified index
Set the torsion-torsion grid at the specified index
Set whether this force should apply periodic boundary conditions when calculating displacements.
Returns whether or not this force makes use of periodic boundary conditions.
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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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void
setUsesPeriodicBoundaryConditions
(bool 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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bool
usesPeriodicBoundaryConditions
() const¶ Returns whether or not this force makes use of periodic boundary conditions.
- Returns
true if force uses PBC and false otherwise
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