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.
usesPeriodicBoundaryConditions((self) -> bool) Returns whether or not this force makes use of periodic boundary conditions.
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:vector< std – grid return grid reference
Return type::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
usesPeriodicBoundaryConditions(self) → bool

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

Returns:true if nonbondedMethod uses PBC and false otherwise
Return type:bool
__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).