AmoebaTorsionTorsionForce
¶

class AmoebaTorsionTorsionForce : public OpenMM::Force¶
This class implements the Amoeba torsiontorsion interaction.
To use it, create an AmoebaTorsionTorsionForce object then call addTorsionTorsion() once for each torsiontorsion. After a torsiontorsion has been added, you can modify its force field parameters by calling setTorsionTorsionParameters().
Public Functions

AmoebaTorsionTorsionForce(void)¶
Create an AmoebaTorsionTorsionForce.

inline int getNumTorsionTorsions(void) const¶
Get the number of torsiontorsion terms in the potential function

inline int getNumTorsionTorsionGrids(void) const¶
Get the number of torsiontorsion grids

int addTorsionTorsion(int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex)¶
Add a torsiontorsion term to the force field.
 Parameters
particle1 – the index of the first particle connected by the torsiontorsion
particle2 – the index of the second particle connected by the torsiontorsion
particle3 – the index of the third particle connected by the torsiontorsion
particle4 – the index of the fourth particle connected by the torsiontorsion
particle5 – the index of the fifth particle connected by the torsiontorsion
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 torsiontorsion that was added

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 torsiontorsion term.
 Parameters
index – the index of the torsiontorsion for which to get parameters
particle1 – [out] the index of the first particle connected by the torsiontorsion
particle2 – [out] the index of the second particle connected by the torsiontorsion
particle3 – [out] the index of the third particle connected by the torsiontorsion
particle4 – [out] the index of the fourth particle connected by the torsiontorsion
particle5 – [out] the index of the fifth particle connected by the torsiontorsion
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

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 torsiontorsion term.
 Parameters
index – the index of the torsiontorsion for which to set parameters
particle1 – the index of the first particle connected by the torsiontorsion
particle2 – the index of the second particle connected by the torsiontorsion
particle3 – the index of the third particle connected by the torsiontorsion
particle4 – the index of the fourth particle connected by the torsiontorsion
particle5 – the index of the fifth particle connected by the torsiontorsion
chiralCheckAtomIndex – the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
gridIndex – the grid index

const std::vector<std::vector<std::vector<double>>> &getTorsionTorsionGrid(int index) const¶
Get the torsiontorsion grid at the specified index
 Parameters
index – the grid index
 Returns
grid return grid reference

void setTorsionTorsionGrid(int index, const std::vector<std::vector<std::vector<double>>> &grid)¶
Set the torsiontorsion grid at the specified index
 Parameters
index – the index of the torsiontorsion 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

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.

virtual bool usesPeriodicBoundaryConditions() const¶
Returns whether or not this force makes use of periodic boundary conditions.
 Returns
true if force uses PBC and false otherwise

AmoebaTorsionTorsionForce(void)¶