RMSDForce

class RMSDForce : public OpenMM::Force

This is a force whose energy equals the root mean squared deviation (RMSD) between the current coordinates and a reference structure. It is intended for use with CustomCVForce. You will not normally want a force that exactly equals the RMSD, but there are many situations where it is useful to have a restraining or biasing force that depends on the RMSD in some way.

The force is computed by first aligning the particle positions to the reference structure, then computing the RMSD between the aligned positions and the reference. The computation can optionally be done based on only a subset of the particles in the system.

Public Functions

explicit RMSDForce(const std::vector<Vec3> &referencePositions, const std::vector<int> &particles = std::vector<int>())

Create an RMSDForce.

Parameters

• referencePositions – the reference positions to compute the deviation from. The length of this vector must equal the number of particles in the system, even if not all particles are used in computing the RMSD.

• particles – the indices of the particles to use when computing the RMSD. If this is empty (the default), all particles in the system will be used.

inline const std::vector<Vec3> &getReferencePositions() const

Get the reference positions to compute the deviation from.

void setReferencePositions(const std::vector<Vec3> &positions)

Set the reference positions to compute the deviation from.

inline const std::vector<int> &getParticles() const

Get the indices of the particles to use when computing the RMSD. If this is empty, all particles in the system will be used.

void setParticles(const std::vector<int> &particles)

Set the indices of the particles to use when computing the RMSD. If this is empty, all particles in the system will be used.

void updateParametersInContext(Context &context)

Update the reference positions and particle indices 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 setReferencePositions() and setParticles() to modify this object’s parameters, then call updateParametersInContext() to copy them over to the Context.

inline 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