CMAPTorsionForce

class CMAPTorsionForce : public OpenMM::Force

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.

Public Functions

CMAPTorsionForce()

Create a CMAPTorsionForce.

inline int getNumMaps() const

Get the number of maps that have been defined.

inline 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 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.

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.

virtual bool usesPeriodicBoundaryConditions() const

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

Returns

true if force uses PBC and false otherwise