AmoebaTorsionTorsionForce

class simtk.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__((self) -> AmoebaTorsionTorsionForce) __init__(self, other) -> AmoebaTorsionTorsionForce
addTorsionTorsion((self, particle1, ...) Add a torsion-torsion term to the force field.
getForceGroup((self) -> int) Get the force group this Force belongs to.
getNumTorsionTorsionGrids((self) -> int) Get the number of torsion-torsion grids
getNumTorsionTorsions((self) -> int) Get the number of torsion-torsion terms in the potential function
getTorsionTorsionGrid((self, index) -> vectorddd) 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.
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) -> bool) Returns whether or not this force makes use of periodic boundary conditions.
__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__sizeof__() → int

size of object in memory, in bytes

__str__
getForceGroup(self) → int

Get the force group this Force belongs to.

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).
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