Literature DB >> 34448578

Adaptive-Partitioning Multilayer Dynamics Simulations: 1. On-the-Fly Switch between Two Quantum Levels of Theory.

Joani Mato1, Adam W Duster1, Emilie B Guidez1, Hai Lin1.   

Abstract

We propose to generalize the previously developed two-layer permuted adaptive-partitioning quantum-mechanics/molecular-mechanics (QM/MM), which reclassifies atoms as QM or MM on-the-fly in dynamics simulations, to multilayer adaptive-partitioning algorithms that enable multiple levels of theory. In this work, we formulate two new algorithms that smoothly interpolate the energy between two QM (Q1 and Q2) levels of theory. The first "permuted adaptive-partitioning" scheme is based on the weighted many-body expansion of the potential, as in the adaptive-partitioning QM/MM. Unconventional and potentially more efficient, the second "interpolated adaptive-partitioning" method employs alchemical QM calculations with Q1/Q2-mixed basis sets, Fock matrices, and overlap matrices. To our knowledge, this is the first time that such alchemical calculations are performed in QM, although they are routinely done in MM. Test calculations on water-cluster models show that both new algorithms indeed yield smooth energy curves when water molecules shift between Q1 and Q2.

Entities:  

Year:  2021        PMID: 34448578      PMCID: PMC8979635          DOI: 10.1021/acs.jctc.1c00556

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.578


  39 in total

1.  Size-Consistent Multipartitioning QM/MM: A Stable and Efficient Adaptive QM/MM Method.

Authors:  Hiroshi C Watanabe; Tomáš Kubař; Marcus Elstner
Journal:  J Chem Theory Comput       Date:  2014-10-14       Impact factor: 6.006

2.  Adaptive switching of interaction potentials in the time domain: an extended Lagrangian approach tailored to transmute force field to QM/MM simulations and back.

Authors:  Marcus Böckmann; Nikos L Doltsinis; Dominik Marx
Journal:  J Chem Theory Comput       Date:  2015-06-09       Impact factor: 6.006

3.  Adaptive-partitioning QM/MM for molecular dynamics simulations: 4. Proton hopping in bulk water.

Authors:  Soroosh Pezeshki; Hai Lin
Journal:  J Chem Theory Comput       Date:  2015-05-22       Impact factor: 6.006

4.  Dual-basis analytic gradients. 1. Self-consistent field theory.

Authors:  Ryan P Steele; Yihan Shao; Robert A DiStasio; Martin Head-Gordon
Journal:  J Phys Chem A       Date:  2006-12-28       Impact factor: 2.781

5.  Extending the power of quantum chemistry to large systems with the fragment molecular orbital method.

Authors:  Dmitri G Fedorov; Kazuo Kitaura
Journal:  J Phys Chem A       Date:  2007-05-19       Impact factor: 2.781

6.  Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials.

Authors:  Jelle M Boereboom; Raffaello Potestio; Davide Donadio; Rosa E Bulo
Journal:  J Chem Theory Comput       Date:  2016-07-11       Impact factor: 6.006

7.  Accurate QM/MM Free Energy Calculations of Enzyme Reactions:  Methylation by Catechol O-Methyltransferase.

Authors:  Thomas H Rod; Ulf Ryde
Journal:  J Chem Theory Comput       Date:  2005-11       Impact factor: 6.006

8.  Explicit Solvation Matters: Performance of QM/MM Solvation Models in Nucleophilic Addition.

Authors:  Jelle M Boereboom; Paul Fleurat-Lessard; Rosa E Bulo
Journal:  J Chem Theory Comput       Date:  2018-03-16       Impact factor: 6.006

9.  Improvement of Performance, Stability and Continuity by Modified Size-Consistent Multipartitioning Quantum Mechanical/Molecular Mechanical Method.

Authors:  Hiroshi C Watanabe
Journal:  Molecules       Date:  2018-07-27       Impact factor: 4.411

10.  Crystal structure of a nitrate/nitrite exchanger.

Authors:  Hongjin Zheng; Goragot Wisedchaisri; Tamir Gonen
Journal:  Nature       Date:  2013-05-12       Impact factor: 49.962

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