Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms
Combined quantum mechanical and molecular mechanical (QM/MM) methods are the most powerful available methods for high-level treatments of subsystems of very large systems. The treatment of the QM−MM boundary strongly affects the accuracy of QM/MM calculations. For QM/MM calculations having covalent...
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| Format: | Article |
| Language: | English |
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MDPI AG
2018-05-01
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| Series: | Molecules |
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| Online Access: | http://www.mdpi.com/1420-3049/23/6/1309 |
| _version_ | 1818217956446830592 |
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| author | Xin-Ping Wu Laura Gagliardi Donald G. Truhlar |
| author_facet | Xin-Ping Wu Laura Gagliardi Donald G. Truhlar |
| author_sort | Xin-Ping Wu |
| collection | DOAJ |
| description | Combined quantum mechanical and molecular mechanical (QM/MM) methods are the most powerful available methods for high-level treatments of subsystems of very large systems. The treatment of the QM−MM boundary strongly affects the accuracy of QM/MM calculations. For QM/MM calculations having covalent bonds cut by the QM−MM boundary, it has been proposed previously to use a scheme with system-specific tuned fluorine link atoms. Here, we propose a broadly parametrized scheme where the parameters of the tuned F link atoms depend only on the type of bond being cut. In the proposed new scheme, the F link atom is tuned for systems with a certain type of cut bond at the QM−MM boundary instead of for a specific target system, and the resulting link atoms are call bond-tuned link atoms. In principle, the bond-tuned link atoms can be as convenient as the popular H link atoms, and they are especially well adapted for high-throughput and accurate QM/MM calculations. Here, we present the parameters for several kinds of cut bonds along with a set of validation calculations that confirm that the proposed bond-tuned link-atom scheme can be as accurate as the system-specific tuned F link-atom scheme. |
| first_indexed | 2024-12-12T07:16:06Z |
| format | Article |
| id | doaj.art-5bec68f3862646f9be06e48df2c385ae |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-12-12T07:16:06Z |
| publishDate | 2018-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-5bec68f3862646f9be06e48df2c385ae2022-12-22T00:33:31ZengMDPI AGMolecules1420-30492018-05-01236130910.3390/molecules23061309molecules23061309Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link AtomsXin-Ping Wu0Laura Gagliardi1Donald G. Truhlar2Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431, USADepartment of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431, USADepartment of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431, USACombined quantum mechanical and molecular mechanical (QM/MM) methods are the most powerful available methods for high-level treatments of subsystems of very large systems. The treatment of the QM−MM boundary strongly affects the accuracy of QM/MM calculations. For QM/MM calculations having covalent bonds cut by the QM−MM boundary, it has been proposed previously to use a scheme with system-specific tuned fluorine link atoms. Here, we propose a broadly parametrized scheme where the parameters of the tuned F link atoms depend only on the type of bond being cut. In the proposed new scheme, the F link atom is tuned for systems with a certain type of cut bond at the QM−MM boundary instead of for a specific target system, and the resulting link atoms are call bond-tuned link atoms. In principle, the bond-tuned link atoms can be as convenient as the popular H link atoms, and they are especially well adapted for high-throughput and accurate QM/MM calculations. Here, we present the parameters for several kinds of cut bonds along with a set of validation calculations that confirm that the proposed bond-tuned link-atom scheme can be as accurate as the system-specific tuned F link-atom scheme.http://www.mdpi.com/1420-3049/23/6/1309electrostaticsmolecular modelingmultiscale modelingQM/MM |
| spellingShingle | Xin-Ping Wu Laura Gagliardi Donald G. Truhlar Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms Molecules electrostatics molecular modeling multiscale modeling QM/MM |
| title | Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms |
| title_full | Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms |
| title_fullStr | Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms |
| title_full_unstemmed | Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms |
| title_short | Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms |
| title_sort | parametrization of combined quantum mechanical and molecular mechanical methods bond tuned link atoms |
| topic | electrostatics molecular modeling multiscale modeling QM/MM |
| url | http://www.mdpi.com/1420-3049/23/6/1309 |
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