Class implementing gmx_mtop_t QMMM modifications during preprocessing 1) Split QM-containing molecules from other molecules in blocks 2) Nullify charges on all virtual sites consisting of QM only atoms 3) Nullifies charges on all QM atoms 4) Excludes LJ interactions between QM atoms 5) Builds vector with atomic numbers of all atoms 6) Makes F_CONNBOND between atoms within QM region 7) Removes angles and settles containing 2 or more QM atoms 8) Removes dihedrals containing 3 or more QM atoms 9) Builds vector containing pairs of bonded QM - MM atoms (Link frontier)
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bool | isQMAtom (Index globalAtomIndex) |
| Retruns true if globalAtomIndex belongs to QM region.
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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.
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void | removeQMClassicalCharges (gmx_mtop_t *mtop) |
| Removes classical charges from QM atoms Provides data about removed charge via topInfo_.
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void | addQMLJExclusions (gmx_mtop_t *mtop) |
| Build exlusion list for LJ interactions between QM atoms.
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void | buildQMMMAtomNumbers (gmx_mtop_t *mtop) |
| Builds atomNumbers_ vector Provides data about total number of QM and MM atoms via topInfo_.
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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_.
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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.
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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_.
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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_.
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void | modifyQMMMVirtualSites (gmx_mtop_t *mtop) |
| Removes charge from all virtual sites which are consists of only QM atoms.
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