#include <gromacs/topology/include/gromacs/topology/embedded_system_preprocessing.h>

Description

Helper class with indexes of broken bonds between embedded and MM.

Used to determine and store pair of embedded and MM atoms between which chemical bond is broken. Also stores the positions of those atoms, and calculates the position of a link atom.

Public Member Functions
	LinkFrontierAtom (int embeddedAtomIndex, int mmAtomIndex)

int	getEmbeddedIndex () const
	Get global index of embedded atom.

int	getMMIndex () const
	Get global index of MM atom.

void	setInputIndices (int inputIndexEmb, int inputIndexMM)
	Set input indices of embedded and MM atoms in the index space of the embedded system.

int	getInputIndexEmb () const
	Get input index of embedded atom in the index space of the embedded system.

int	getInputIndexMM () const
	Get input index of MM atom in the index space of the embedded system.

void	setPositions (const RVec &posEmb, const RVec &posMM)
	Set positions of embedded and MM atoms and calculate position of link atom.

RVec	getLinkPosition () const
	Get position of link atom.

std::tuple< RVec, RVec >	spreadForce (const RVec &fl, const t_pbc &pbc) const
	Redistribute force on link atom to embedded and MM atoms.

real	linkDistance () const

void	setLinkDistance (const real &linkDistance)

int	linkAtomNumber () const

void	setLinkAtomNumber (const int &linkAtomNumber)

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

src/gromacs/topology/include/gromacs/topology/embedded_system_preprocessing.h
src/gromacs/topology/embedded_system_preprocessing.cpp

Description

Public Member Functions