Description

Class responsible for all modifications of the topology during input pre-processing.

Inherits from QMMMTopologyPreprocessor and performs the following modifications for a scheme analoguous to mechanical embedding in QMMM: 1) Split molecules containing NNP input atoms from other molecules in blocks 2) Exclude non-bonded interactions between NNP atoms. 3) Build vector with atomic numbers of all atoms. 4) Make F_CONNBOND between atoms within NNP region. 5) Remove angles and settles containing 2 or more NNP atoms. 6) Remove dihedrals containing 3 or more NNP atoms.

Public Member Functions
	NNPotTopologyPreprocessor (ArrayRef< const Index > inputIndices)
	Constructor for NNPotTopologyPreprocessor from its parameters. More...

void	preprocess (gmx_mtop_t *mtop)
	Process mtop topology and builds topInfo_ containing information about topology modifications. More...

Public Member Functions inherited from gmx::QMMMTopologyPreprocessor
	QMMMTopologyPreprocessor (ArrayRef< const Index > qmIndices)
	Constructor for QMMMTopologyPreprocessor from its parameters. More...

void	preprocess (gmx_mtop_t *mtop)
	Pocesses mtop topology and prepares atomNumbers_ and linkFrontier_ vectors Builds topInfo_ containing information about topology modifications. More...

const QMMMTopologyInfo &	topInfo () const
	Returns data about modifications made via QMMMTopologyInfo.

ArrayRef< const int >	atomNumbers () const
	Returns view of atomic numbers for all atoms in the processed topology.

ArrayRef< const real >	atomCharges () const
	Returns view of point charges for all atoms in the processed topology.

ArrayRef< const LinkFrontier >	linkFrontier () const
	Returns view of the whole Link Frontier for the processed topology.

Additional Inherited Members
Protected Member Functions inherited from gmx::QMMMTopologyPreprocessor
bool	isQMAtom (Index globalAtomIndex)
	Retruns true if globalAtomIndex belongs to QM region.

void	splitQMblocks (gmx_mtop_t *mtop)
	Splits QM containing molecules out of MM blocks in topology Modifies blocks in topology Updates bQMBlock vector containing QM flags of all blocks in modified mtop.

void	removeQMClassicalCharges (gmx_mtop_t *mtop)
	Removes classical charges from QM atoms Provides data about removed charge via topInfo_.

void	addQMLJExclusions (gmx_mtop_t *mtop)
	Build exlusion list for LJ interactions between QM atoms.

void	buildQMMMAtomNumbers (gmx_mtop_t *mtop)
	Builds atomNumbers_ vector Provides data about total number of QM and MM atoms via topInfo_.

void	modifyQMMMTwoCenterInteractions (gmx_mtop_t *mtop)
	Modifies pairwise bonded interactions Removes any other pairwise bonded interactions between QM-QM atoms Creates F_CONNBOND between QM atoms Any restraints and constraints will be kept Provides data about modifications via topInfo_.

void	buildQMMMLink (gmx_mtop_t *mtop)
	Builds link_ vector with pairs of atoms indicting broken QM - MM chemical bonds. Also performs search of constrained bonds within QM subsystem.

void	modifyQMMMThreeCenterInteractions (gmx_mtop_t *mtop)
	Modifies three-centers interactions (i.e. Angles, Settles) Removes any other three-centers bonded interactions including 2 or more QM atoms Any restraints and constraints will be kept Any F_SETTLE containing QM atoms will be converted to the pair of F_CONNBONDS Provides data about modifications via topInfo_.

void	modifyQMMMFourCenterInteractions (gmx_mtop_t *mtop)
	Modifies four-centers interactions Removes any other four-centers bonded interactions including 3 or more QM atoms Any restraints and constraints will be kept Provides data about modifications via topInfo_.

void	modifyQMMMVirtualSites (gmx_mtop_t *mtop)
	Removes charge from all virtual sites which are consists of only QM atoms.

Constructor & Destructor Documentation

gmx::NNPotTopologyPreprocessor::NNPotTopologyPreprocessor ( ArrayRef< const Index > inputIndices )

Constructor for NNPotTopologyPreprocessor from its parameters.

Parameters

[in] inputIndices Array with global indices of NN input atoms

Member Function Documentation

void gmx::NNPotTopologyPreprocessor::preprocess ( gmx_mtop_t * mtop )

Process mtop topology and builds topInfo_ containing information about topology modifications.

Parameters

[in,out] mtop Topology that needs to be modified

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

src/gromacs/applied_forces/nnpot/nnpottopologypreprocessor.h
src/gromacs/applied_forces/nnpot/nnpottopologypreprocessor.cpp

Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation