Literature DB >> 27782640

TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field.

Jacek Dziedzic1, Yuezhi Mao2, Yihan Shao3, Jay Ponder4, Teresa Head-Gordon2, Martin Head-Gordon2, Chris-Kriton Skylaris1.   

Abstract

We present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression for the Hamiltonian of the coupled QM/MM system, which we minimize using gradient methods. The QM subsystem is described by the onetep linear-scaling DFT approach, which makes use of strictly localized orbitals expressed in a set of periodic sinc basis functions equivalent to plane waves. The MM subsystem is described by the multipolar, polarizable force field AMOEBA, as implemented in tinker. Distributed multipole analysis is used to obtain, on the fly, a classical representation of the QM subsystem in terms of atom-centered multipoles. This auxiliary representation is used for all polarization interactions between QM and MM, allowing us to treat them on the same footing as in AMOEBA. We validate our method in tests of solute-solvent interaction energies, for neutral and charged molecules, demonstrating the simultaneous optimization of the quantum and classical degrees of freedom. Encouragingly, we find that the inclusion of explicit polarization in the MM part of QM/MM improves the agreement with fully QM calculations.

Year:  2016        PMID: 27782640     DOI: 10.1063/1.4962909

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  9 in total

1.  An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

Authors:  Jing Huang; Ye Mei; Gerhard König; Andrew C Simmonett; Frank C Pickard; Qin Wu; Lee-Ping Wang; Alexander D MacKerell; Bernard R Brooks; Yihan Shao
Journal:  J Chem Theory Comput       Date:  2017-01-24       Impact factor: 6.006

2.  A Many-Body, Fully Polarizable Approach to QM/MM Simulations.

Authors:  Eleftherios Lambros; Filippo Lipparini; Gerardo Andrés Cisneros; Francesco Paesani
Journal:  J Chem Theory Comput       Date:  2020-11-19       Impact factor: 6.006

3.  Mapping the Drude polarizable force field onto a multipole and induced dipole model.

Authors:  Jing Huang; Andrew C Simmonett; Frank C Pickard; Alexander D MacKerell; Bernard R Brooks
Journal:  J Chem Phys       Date:  2017-10-28       Impact factor: 3.488

4.  Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields.

Authors:  Ye Ding; You Xu; Cheng Qian; Jinfeng Chen; Jian Zhu; Houhou Huang; Yi Shi; Jing Huang
Journal:  J Comput Aided Mol Des       Date:  2020-01-20       Impact factor: 3.686

Review 5.  Advanced Potential Energy Surfaces for Molecular Simulation.

Authors:  Alex Albaugh; Henry A Boateng; Richard T Bradshaw; Omar N Demerdash; Jacek Dziedzic; Yuezhi Mao; Daniel T Margul; Jason Swails; Qiao Zeng; David A Case; Peter Eastman; Lee-Ping Wang; Jonathan W Essex; Martin Head-Gordon; Vijay S Pande; Jay W Ponder; Yihan Shao; Chris-Kriton Skylaris; Ilian T Todorov; Mark E Tuckerman; Teresa Head-Gordon
Journal:  J Phys Chem B       Date:  2016-09-22       Impact factor: 3.466

6.  Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials.

Authors:  Jorge Nochebuena; Sehr Naseem-Khan; G Andrés Cisneros
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2021-01-12

7.  Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations.

Authors:  Xiaoliang Pan; Edina Rosta; Yihan Shao
Journal:  Molecules       Date:  2018-09-29       Impact factor: 4.411

8.  A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes.

Authors:  Gerhard König; Frank C Pickard; Jing Huang; Walter Thiel; Alexander D MacKerell; Bernard R Brooks; Darrin M York
Journal:  Molecules       Date:  2018-10-19       Impact factor: 4.411

9.  Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings.

Authors:  Daniele Loco; Louis Lagardère; Gérardo A Cisneros; Giovanni Scalmani; Michael Frisch; Filippo Lipparini; Benedetta Mennucci; Jean-Philip Piquemal
Journal:  Chem Sci       Date:  2019-06-11       Impact factor: 9.825

  9 in total

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