CMAPTorsionForce¶

class
OpenMM::
CMAPTorsionForce
¶ 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 callingaddTorsion()
. 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.Methods
CMAPTorsionForce
Create a CMAPTorsionForce
.getNumMaps
Get the number of maps that have been defined. getNumTorsions
Get the number of CMAP torsion terms in the potential function addMap
Create a new map that can be used for torsion pairs. getMapParameters
Get the energy values of a map. setMapParameters
Set the energy values of a map. addTorsion
Add a CMAP torsion term to the force field. getTorsionParameters
Get the force field parameters for a CMAP torsion term. setTorsionParameters
Set the force field parameters for a CMAP torsion term. updateParametersInContext
Update the map and torsion parameters in a Context
to match those stored in thisForce
object.setUsesPeriodicBoundaryConditions
Set whether this force should apply periodic boundary conditions when calculating displacements. usesPeriodicBoundaryConditions
Returns whether or not this force makes use of periodic boundary conditions. 
CMAPTorsionForce
()¶ Create a
CMAPTorsionForce()
.

int
getNumMaps
() const¶ Get the number of maps that have been defined.

int
getNumTorsions
() const¶ Get the number of CMAP torsion terms in the potential function

int
addMap
(int size, const std::vector<double> &energy)¶ Create a new map that can be used for torsion pairs.
Parameters:  size – the size of the map along each dimension
 energy – 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

void
getMapParameters
(int index, int &size, std::vector<double> &energy) const¶ Get the energy values of a map.
Parameters:  index – the index of the map for which to get energy values
 size – [out] the size of the map along each dimension
 energy – [out] 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.

void
setMapParameters
(int index, int size, const std::vector<double> &energy)¶ Set the energy values of a map.
Parameters:  index – the index of the map for which to set energy values
 size – the size of the map along each dimension
 energy – 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.

int
addTorsion
(int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4)¶ Add a CMAP torsion term to the force field.
Parameters:  map – the index of the map to use for this term
 a1 – the index of the first particle forming the first torsion
 a2 – the index of the second particle forming the first torsion
 a3 – the index of the third particle forming the first torsion
 a4 – the index of the fourth particle forming the first torsion
 b1 – the index of the first particle forming the second torsion
 b2 – the index of the second particle forming the second torsion
 b3 – the index of the third particle forming the second torsion
 b4 – the index of the fourth particle forming the second torsion
Returns: the index of the torsion that was added

void
getTorsionParameters
(int index, int &map, int &a1, int &a2, int &a3, int &a4, int &b1, int &b2, int &b3, int &b4) const¶ Get the force field parameters for a CMAP torsion term.
Parameters:  index – the index of the torsion for which to get parameters
 map – [out] the index of the map to use for this term
 a1 – [out] the index of the first particle forming the first torsion
 a2 – [out] the index of the second particle forming the first torsion
 a3 – [out] the index of the third particle forming the first torsion
 a4 – [out] the index of the fourth particle forming the first torsion
 b1 – [out] the index of the first particle forming the second torsion
 b2 – [out] the index of the second particle forming the second torsion
 b3 – [out] the index of the third particle forming the second torsion
 b4 – [out] the index of the fourth particle forming the second torsion

void
setTorsionParameters
(int index, int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4)¶ Set the force field parameters for a CMAP torsion term.
Parameters:  index – the index of the torsion for which to set parameters
 map – the index of the map to use for this term
 a1 – the index of the first particle forming the first torsion
 a2 – the index of the second particle forming the first torsion
 a3 – the index of the third particle forming the first torsion
 a4 – the index of the fourth particle forming the first torsion
 b1 – the index of the first particle forming the second torsion
 b2 – the index of the second particle forming the second torsion
 b3 – the index of the third particle forming the second torsion
 b4 – the index of the fourth particle forming the second torsion

void
updateParametersInContext
(Context &context)¶ Update the map and torsion parameters in a
Context
to match those stored in thisForce
object. This method provides an efficient method to update certain parameters in an existingContext
without needing to reinitialize it. Simply callsetMapParameters()
andsetTorsionParameters()
to modify this object’s parameters, then callupdateParametersInContext()
to copy them over to theContext
.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.

void
setUsesPeriodicBoundaryConditions
(bool 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.

bool
usesPeriodicBoundaryConditions
() const¶ Returns whether or not this force makes use of periodic boundary conditions.
Returns: true if force uses PBC and false otherwise
