Dihedral angle potentials

namespace mdk
class DihedralAngles : public mdk::Force
#include <DihedralAngles.hpp>

A force field for dihedral angles, composed of:

  • the “native” part, which exists in two mutually exclusive variants (simple and complex);

  • the “heurestic” part. The native part supercedes heurestic part whenever native dihedral angle is defined for a quadruple.

Public Functions

virtual void bind(Simulation &simulation) override

Bind the force field to a simulation.

Parameters

simulation – Simulation to bind to.

virtual void asyncPart(Dynamics &dynamics) override

“Asynchronous” part of the potential. Here it’s the only part.

Parameters

dynamics – Dynamics object to add potential energy and forces to.

Private Members

std::variant<std::monostate, ComplexNativeDihedral*, SimpleNativeDihedral*> natDih = std::monostate()

The “native” part, i.e. either nothing, complex variant or the simple variant.

HeuresticDihedral *heurDih = nullptr

The “heurestic” part of the potential.

Bytes inRange

Friends

friend class ComplexNativeDihedral
friend class SimpleNativeDihedral
friend class HeuresticDihedral
namespace mdk
class NativeDihedralBase : public mdk::SimulVar
#include <NativeDihedralBase.hpp>

A common part of simple and complex native dihedral variants. In particular, it stores whether a quadruple (i-2, i-1, i, i+1) has an associated native dihedral angle, and its value if it is the case.

Subclassed by mdk::ComplexNativeDihedral, mdk::SimpleNativeDihedral

Public Functions

virtual void bind(Simulation &simulation) override

Bind the variant to the simulation. Technically one shouldn’t add this base to the simulation itself; it serves as a prototype for bind in ComplexNativeDihedral and SimpleNativeDihedral in particular, it retrieves and computes isNative and phi0.

Parameters

simulation –

Protected Attributes

Bytes isNative

isNative[i] = 1 if a quadruple (i-2, i-1, i, i+1) has an associated native dihedral angle, 0 otherwise.

Scalars phi0

phi0[i] has the value of an associated native dihedral angle, if such exists for the quadruple (i-2, i-1, i, i+1); otherwise, the value is undefined.

namespace mdk
class ComplexNativeDihedral : public mdk::NativeDihedralBase
#include <ComplexNativeDihedral.hpp>

The complex variant of the native part of the dihedral angle potential.

Public Functions

virtual void bind(Simulation &simulation) override

Bind the part to the simulation - in particular, find (and possibly create) DihedralAngles force field and add itself to it.

Parameters

simulation – Simulation to bind to.

inline void term(int i, double phi, double &V, double &dV_dphi) const

Term of the formula for the dihedral angle potential of a single quadruple. Note: it’s inline in order for the compiler to inline it in DihedralAngles.cpp file.

Parameters

  • i – The index i in the quadruple (i-2, i-1, i, i+1).

  • phi – Dihedral angle between planes defined by sequences i-2, i-1, i and i-1, i, i+1.

  • V – Potential energy reference to add to.

  • dV_dphi – Derivative of potential energy wrt the angle phi to add to.

Public Members

double CDA = 0.66 * eps / pow(rad, 2.0)
double CDB = 0.66 * eps / pow(rad, 2.0)

Friends

friend class DihedralAngles
namespace mdk
class SimpleNativeDihedral : public mdk::NativeDihedralBase
#include <SimpleNativeDihedral.hpp>

The simple variant of the native part of the dihedral angle potential.

Public Functions

virtual void bind(Simulation &simulation) override

Bind the part to the simulation - in particular, find (and possibly create) DihedralAngles force field and add itself to it.

Parameters

simulation – Simulation to bind to.

inline void term(int i, double phi, double &V, double &dV_dphi) const

Term of the formula for the dihedral angle potential of a single quadruple. Note: it’s inline in order for the compiler to inline it in DihedralAngles.cpp file.

Parameters

  • i – The index i in the quadruple (i-2, i-1, i, i+1).

  • phi – Dihedral angle between planes defined by sequences i-2, i-1, i and i-1, i, i+1.

  • V – Potential energy reference to add to.

  • dV_dphi – Derivative of potential energy wrt the angle phi to add to.

Public Members

double CDH = 3.33 * eps / pow(rad, 2)

Friends

friend class DihedralAngles
namespace mdk
class HeuresticDihedral : public mdk::SimulVar
#include <HeuresticDihedral.hpp>

Heurestic part of the dihedral potential, applied when with the quadruple (i-2, i-1, i, i+1) is not associated a native dihedral angle.

Public Functions

virtual void bind(Simulation &simulation) override

Bind the part to the simulation - in particular, find (and possibly create) DihedralAngles force field and add itself to it.

Parameters

simulation – Simulation to bind to.

inline void term(int i, double phi, double &V, double &dV_dphi) const

Term of the formula for the dihedral angle potential of a single quadruple. Note: it’s inline in order for the compiler to inline it in DihedralAngles.cpp file.

Parameters

  • i – The index i in the quadruple (i-2, i-1, i, i+1).

  • phi – Dihedral angle between planes defined by sequences i-2, i-1, i and i-1, i, i+1.

  • V – Potential energy reference to add to.

  • dV_dphi – Derivative of potential energy wrt the angle phi to add to.

Private Members

double coeff[numOfPTs][6]

Coefficients per pair type (where pair is (i-1, i) from the quadruple.

Eigen::Matrix<int8_t, Eigen::Dynamic, 1> angleTypes

Types of angles (i.e. pair types for each pair (i-1, i)).

Friends

friend class DihedralAngles