AmoebaTorsionTorsionForce

class OpenMM::AmoebaTorsionTorsionForce

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().

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
setUsesPeriodicBoundaryConditions Set whether this force should apply periodic boundary conditions when calculating displacements.
usesPeriodicBoundaryConditions Returns whether or not this force makes use of periodic boundary conditions.
AmoebaTorsionTorsionForce(void)

Create an AmoebaTorsionTorsionForce().

int getNumTorsionTorsions(void) const

Get the number of torsion-torsion terms in the potential function

int getNumTorsionTorsionGrids(void) const

Get the number of torsion-torsion grids

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
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
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
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
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
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.

bool usesPeriodicBoundaryConditions() const

Returns whether or not this force makes use of periodic boundary conditions.

Returns:true if force uses PBC and false otherwise