SimTK::DuMM::CustomBondTorsion Class Reference

Abstract base class for custom torsion functions, that is, functional forms that apply a dihedral-angle based torque about the middle bond of a 1-2-3-4 quadruple of bonded atoms. More...

#include <DuMMForceFieldSubsystem.h>

List of all members.

Public Member Functions
virtual	~CustomBondTorsion ()
virtual Real	calcEnergy (Real dihedralAngle) const =0
virtual Real	calcTorque (Real dihedralAngle) const =0

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Detailed Description

Abstract base class for custom torsion functions, that is, functional forms that apply a dihedral-angle based torque about the middle bond of a 1-2-3-4 quadruple of bonded atoms.

AmberTorsion example

This demonstrates how the built-in Amber force might be applied as a custom torsion. This is a toy example because this particular form is already built into DuMMForceFieldSubsystem.

 class AmberTorsion : public DuMM::CustomBondTorsion {
 public:
    AmberTorsion(Real amplitudeInKJ, Real phaseInRad, int periodicity)
    :   amplitude(amplitudeInKJ), phase(phaseInRad), periodicity(periodicity) {}
 
    Real calcEnergy(Real dihedralAngleInRad) {
        return amplitude * 
                  ( 1 + std::cos(periodicity * dihedralAngleInRad - phase) );
    }

    // Note: this is MINUS the gradient of the energy function!
    Real calcTorque(Real dihedralAngleInRad) {
        return periodicity * amplitude * 
                  std::sin(periodicity * dihedralAngleInRad - phase);
    }

 private:
    Real amplitude;       // in KJ/mol
    Real phase;           // in radians
    int  periodicity;
 };
 
 #include "SimTKmolmodel.h"
 int main() {
     DuMMForceFieldSubsystem dumm;
     dumm.loadAmber99Parameters();
     // torsion for aliphatic H-C-C-H torsions like those in ethane
     dumm.defineCustomTorsion(
         dumm.getAtomClassIndex("HC"),
         dumm.getAtomClassIndex("CT"),
         dumm.getAtomClassIndex("CT"),
         dumm.getAtomClassIndex("HC"),
         new AmberTorsion(0.150*DuMM::Kcal2KJ, 0*DuMM::Deg2Rad, 3));
     ...
 }

See also:

DuMMForceFieldSubsystem::defineCustomBondTorsion()

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Constructor & Destructor Documentation

virtual SimTK::DuMM::CustomBondTorsion::~CustomBondTorsion

(

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[inline, virtual]

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The documentation for this class was generated from the following file:

• DuMMForceFieldSubsystem.h