Sidechain Lennard-Jones potential kernel¶
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class mdk::SidechainLJ
Sidechain version of the L-J potential (for a single pair of
depthandsink_max). In the CPC14.pdf it’s described as an L-J potential with a well bounded from both ends; in practice this is implemented as a one-sided well, i.e. for r < sink_max, V = - depth and the other side of the well is handled by the Pauli exclusion.Public Functions
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SidechainLJ() = default
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inline SidechainLJ(double depth, double sink_max)
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inline double cutoff() const
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inline void computeV(double norm, double &V, double &dV_dn) const
Compute the potential energy of the force field.
- Parameters
norm – Distance between the residues.
V – Variable to add the potential to.
dV_dn – Variable to add the derivative to.
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template<typename T1, typename T2>
inline void computeF(VRef unit, double norm, double &V, T1 F1, T2 F2) const Compute and add the L-J force between two residues. The templates are here in order for us to be able to pass Eigen expressions to it.
- Template Parameters
T1 – Type of an lvalue to add the force on the first residue to.
T2 – Type of an lvalue to add the force on the second residue to.
- Parameters
unit – Normalized vector between the residues.
norm – Distance between the residues.
V – Variable to add the potential to.
F1 – Lvalue to add the force on the first residue to.
F2 – Lvalue to add the force on the second residue to.
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SidechainLJ() = default