Electrostatic forces¶
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namespace mdk
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class ESBase : public mdk::NonlocalForce
- #include <ESBase.hpp>
A base class for the Debye-Hueckel screened electrostatic potentials.
Subclassed by mdk::ConstDH, mdk::RelativeDH
Public Functions
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virtual void bind(Simulation &simulation) override
Bind the class to the simulation. It initializes
chargeand adds the force to the VL list. Note: this class (ESBase) shouldn’t be added to the simulation class, only the derived classes.- Parameters
simulation – Simulation to bind to.
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virtual void vlUpdateHook() override
An action to be performed when the Verlet list is updated. Here we want to recreate
pairs, i.e. filter the Verlet list so that only charged pairs are present.
Protected Attributes
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std::vector<Contact> pairs
A local, filtered Verlet list of pairs. Since most residues are not charged, and pairs even moreso, it benefits us to keep a local list and not check the pairs which we would know cannot interact with each other.
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Eigen::Matrix<int8_t, Eigen::Dynamic, 1> charge
A list of charges of the residues (in units of
echarge).
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struct Contact
- #include <ESBase.hpp>
A struct detailing a contact between pairs. We store the indices and the product of the charges.
Public Members
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int i1
Index of the first residue.
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int i2
Index of the second residue.
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double q1_x_q2
Product of residues’ charges.
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int i1
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virtual void bind(Simulation &simulation) override
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class ESBase : public mdk::NonlocalForce
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namespace mdk