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