embedded_system_preprocessing.h File Reference

#include <set>
#include <vector>
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/vectypes.h"

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Description

Collection of topology preprocessing functions responsible for all modifications of the topology during input pre-processing when a part of the system is handled outside the classical MM approximation (e.g. QM/MM or neural-network/MM).

Author

Lukas Müllender lukas.nosp@m..mue.nosp@m.llend.nosp@m.er@g.nosp@m.mail..nosp@m.com

Classes
class	gmx::LinkFrontierAtom
	Helper class with indexes of broken bonds between embedded and MM. More...

Functions
std::vector< bool >	gmx::splitEmbeddedBlocks (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices)
	Splits embedded atom containing molecules out of MM blocks in topology. More...
std::vector< real >	gmx::removeEmbeddedClassicalCharges (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const std::vector< bool > &isEmbeddedBlock, real refQ, const MDLogger &logger, WarningHandler *wi)
	Removes classical charges from embedded atoms and virtual sites. More...
void	gmx::addEmbeddedNBExclusions (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const MDLogger &logger)
	Build exclusion list for non-bonded interactions between embedded atoms. More...
std::vector< int >	gmx::buildEmbeddedAtomNumbers (const gmx_mtop_t &mtop)
	Builds and returns a vector of atom numbers for all atoms in mtop. More...
void	gmx::modifyEmbeddedTwoCenterInteractions (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const std::vector< bool > &isEmbeddedBlock, const MDLogger &logger)
	Modifies pairwise bonded interactions. More...
void	gmx::modifyEmbeddedThreeCenterInteractions (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const std::vector< bool > &isEmbeddedBlock, const MDLogger &logger)
	Modifies three-centers interactions (i.e. Angles, Settles) More...
void	gmx::modifyEmbeddedFourCenterInteractions (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const std::vector< bool > &isEmbeddedBlock, const MDLogger &logger)
	Modifies four-centers interactions. More...
void	gmx::checkConstrainedBonds (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const std::vector< bool > &isEmbeddedBlock, WarningHandler *wi)
	Checks for constrained bonds within embedded subsystem. More...
std::vector< LinkFrontierAtom >	gmx::buildLinkFrontier (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const std::vector< bool > &isEmbeddedBlock, const MDLogger &logger)
	Builds link frontier vector with pairs of atoms indicting broken embedded - MM chemical bonds. More...