Molmodel
Classes

User defined molecular mechanics force terms

Molecular Mechanics in Molmodel

These classes are used with DuMMForceFieldSubsystem to permit user-defined functional forms for bonded terms. More...

Classes

class  SimTK::DuMM::CustomBondStretch
 Abstract base class for custom bond stretch terms, that is, functional forms that apply a distance-based force along a 1-2 bond between a pair of atoms. More...
class  SimTK::DuMM::CustomBondBend
 Abstract base class for custom bond bend functions, that is, functional forms that apply an angle-based torque between the two lines formed by a 1-2-3 triple of bonded atoms. More...
class  SimTK::DuMM::CustomBondTorsion
 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...

Detailed Description

These classes are used with DuMMForceFieldSubsystem to permit user-defined functional forms for bonded terms.

Basic features

Notes

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));
     ...
 }
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