CMAPTorsionForce

class simtk.openmm.openmm.CMAPTorsionForce(*args)

This class implements an interaction between pairs of dihedral angles. The interaction energy is defined by an “energy correction map” (CMAP), which is simply a set of tabulated energy values on a regular grid of (phi, psi) angles. Natural cubic spline interpolation is used to compute forces and energies at arbitrary values of the two angles.

To use this class, first create one or more energy correction maps by calling addMap(). For each one, you provide an array of energies at uniformly spaced values of the two angles. Next, add interactions by calling addTorsion(). For each one, you specify the sequence of particles used to calculate each of the two dihedral angles, and the index of the map used to calculate their interaction energy.

__init__(self) → CMAPTorsionForce

__init__(self, other) -> CMAPTorsionForce

Create a CMAPTorsionForce.

Methods

__init__((self) -> CMAPTorsionForce) __init__(self, other) -> CMAPTorsionForce
addMap((self, size, energy) -> int) Create a new map that can be used for torsion pairs.
addTorsion((self, map, a1, a2, a3, a4, b1, ...) Add a CMAP torsion term to the force field.
getForceGroup((self) -> int) Get the force group this Force belongs to.
getMapParameters(self, index) Get the energy values of a map.
getNumMaps((self) -> int) Get the number of maps that have been defined.
getNumTorsions((self) -> int) Get the number of CMAP torsion terms in the potential function
getTorsionParameters(self, index) Get the force field parameters for a CMAP torsion term.
setForceGroup(self, group) Set the force group this Force belongs to.
setMapParameters(self, index, size, energy) Set the energy values of a map.
setTorsionParameters(self, index, map, a1, ...) Set the force field parameters for a CMAP torsion term.
setUsesPeriodicBoundaryConditions(self, periodic) Set whether this force should apply periodic boundary conditions when calculating displacements.
updateParametersInContext(self, context) Update the map and torsion parameters in a Context to match those stored in this Force object.
usesPeriodicBoundaryConditions((self) -> bool) Returns whether or not this force makes use of periodic boundary conditions.
getNumMaps(self) → int

Get the number of maps that have been defined.

getNumTorsions(self) → int

Get the number of CMAP torsion terms in the potential function

addMap(self, size, energy) → int

Create a new map that can be used for torsion pairs.

Parameters:
  • size (int) – the size of the map along each dimension
  • energy (vector< double >) – the energy values for the map. This must be of length size*size. The element energy[i+size*j] contains the energy when the first torsion angle equals i*2*PI/size and the second torsion angle equals j*2*PI/size.
Returns:

the index of the map that was added

Return type:

int

getMapParameters(self, index)

Get the energy values of a map.

Parameters:index (int) – the index of the map for which to get energy values
Returns:
  • size (int) – the size of the map along each dimension
  • energy (vector< double >) – the energy values for the map. This must be of length size*size. The element energy[i+size*j] contains the energy when the first torsion angle equals i*2*PI/size and the second torsion angle equals j*2*PI/size.
setMapParameters(self, index, size, energy)

Set the energy values of a map.

Parameters:
  • index (int) – the index of the map for which to set energy values
  • size (int) – the size of the map along each dimension
  • energy (vector< double >) – the energy values for the map. This must be of length size*size. The element energy[i+size*j] contains the energy when the first torsion angle equals i*2*PI/size and the second torsion angle equals j*2*PI/size.
addTorsion(self, map, a1, a2, a3, a4, b1, b2, b3, b4) → int

Add a CMAP torsion term to the force field.

Parameters:
  • map (int) – the index of the map to use for this term
  • a1 (int) – the index of the first particle forming the first torsion
  • a2 (int) – the index of the second particle forming the first torsion
  • a3 (int) – the index of the third particle forming the first torsion
  • a4 (int) – the index of the fourth particle forming the first torsion
  • b1 (int) – the index of the first particle forming the second torsion
  • b2 (int) – the index of the second particle forming the second torsion
  • b3 (int) – the index of the third particle forming the second torsion
  • b4 (int) – the index of the fourth particle forming the second torsion
Returns:

the index of the torsion that was added

Return type:

int

getTorsionParameters(self, index)

Get the force field parameters for a CMAP torsion term.

Parameters:index (int) – the index of the torsion for which to get parameters
Returns:
  • map (int) – the index of the map to use for this term
  • a1 (int) – the index of the first particle forming the first torsion
  • a2 (int) – the index of the second particle forming the first torsion
  • a3 (int) – the index of the third particle forming the first torsion
  • a4 (int) – the index of the fourth particle forming the first torsion
  • b1 (int) – the index of the first particle forming the second torsion
  • b2 (int) – the index of the second particle forming the second torsion
  • b3 (int) – the index of the third particle forming the second torsion
  • b4 (int) – the index of the fourth particle forming the second torsion
setTorsionParameters(self, index, map, a1, a2, a3, a4, b1, b2, b3, b4)

Set the force field parameters for a CMAP torsion term.

Parameters:
  • index (int) – the index of the torsion for which to set parameters
  • map (int) – the index of the map to use for this term
  • a1 (int) – the index of the first particle forming the first torsion
  • a2 (int) – the index of the second particle forming the first torsion
  • a3 (int) – the index of the third particle forming the first torsion
  • a4 (int) – the index of the fourth particle forming the first torsion
  • b1 (int) – the index of the first particle forming the second torsion
  • b2 (int) – the index of the second particle forming the second torsion
  • b3 (int) – the index of the third particle forming the second torsion
  • b4 (int) – the index of the fourth particle forming the second torsion
updateParametersInContext(self, context)

Update the map and torsion parameters in a Context to match those stored in this Force object. This method provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it. Simply call setMapParameters() and setTorsionParameters() to modify this object’s parameters, then call updateParametersInContext() to copy them over to the Context.

The only information that can be updated with this method is the energy values for a map, and the map index for a torsion. The size of a map and the set of particles involved in a torsion cannot be changed. Also, new bonds and torsions cannot be added.

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
__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).