AmoebaTorsionTorsionForce

class 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().

__init__(self)AmoebaTorsionTorsionForce
__init__(self, other)AmoebaTorsionTorsionForce

Create an AmoebaTorsionTorsionForce.

Methods

__init__(-> AmoebaTorsionTorsionForce)

Create an AmoebaTorsionTorsionForce.

addTorsionTorsion(self, particle1, …)

Add a torsion-torsion term to the force field.

getForceGroup(self)

Get the force group this Force belongs to.

getName(self)

Get the name of this Force.

getNumTorsionTorsionGrids(self)

Get the number of torsion-torsion grids

getNumTorsionTorsions(self)

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

getTorsionTorsionGrid(self, index)

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.

setName(self, name)

Set the name of this Force.

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)

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

Attributes

thisown

The membership flag

property thisown

The membership flag

getNumTorsionTorsions(self)int

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

getNumTorsionTorsionGrids(self)int

Get the number of torsion-torsion grids

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

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

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

getTorsionTorsionGrid(self, index)vectorddd

Get the torsion-torsion grid at the specified index

Parameters

index (int) – the grid index

Returns

grid return grid reference

Return type

vector< std::vector< std::vector< double > > >

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

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.

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

getForceGroup(self)int

Get the force group this Force belongs to.

getName(self)std::string const &

Get the name of this Force. This is an arbitrary, user modifiable identifier. By default it equals the class name, but you can change it to anything useful.

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).

setName(self, name)

Set the name of this Force. This is an arbitrary, user modifiable identifier. By default it equals the class name, but you can change it to anything useful.