Literature DB >> 22089416

QM/MM simulation of liquid water with an adaptive quantum region.

Noam Bernstein1, Csilla Várnai, Iván Solt, Steven A Winfield, Mike C Payne, István Simon, Mónika Fuxreiter, Gábor Csányi.   

Abstract

The simulation of complex chemical systems often requires a multi-level description, in which a region of special interest is treated using a computationally expensive quantum mechanical (QM) model while its environment is described by a faster, simpler molecular mechanical (MM) model. Furthermore, studying dynamic effects in solvated systems or bio-molecules requires a variable definition of the two regions, so that atoms or molecules can be dynamically re-assigned between the QM and MM descriptions during the course of the simulation. Such reassignments pose a problem for traditional QM/MM schemes by exacerbating the errors that stem from switching the model at the boundary. Here we show that stable, long adaptive simulations can be carried out using density functional theory with the BLYP exchange-correlation functional for the QM model and a flexible TIP3P force field for the MM model without requiring adjustments of either. Using a primary benchmark system of pure water, we investigate the convergence of the liquid structure with the size of the QM region, and demonstrate that by using a sufficiently large QM region (with radius 6 Å) it is possible to obtain radial and angular distributions that, in the QM region, match the results of fully quantum mechanical calculations with periodic boundary conditions, and, after a smooth transition, also agree with fully MM calculations in the MM region. The key ingredient is the accurate evaluation of forces in the QM subsystem which we achieve by including an extended buffer region in the QM calculations. We also show that our buffered-force QM/MM scheme is transferable by simulating the solvated Cl(-) ion.

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Year:  2011        PMID: 22089416     DOI: 10.1039/c1cp22600b

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  11 in total

1.  Accelerated Computation of Free Energy Profile at Ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference Potential. 4. Adaptive QM/MM.

Authors:  Jia-Ning Wang; Wei Liu; Pengfei Li; Yan Mo; Wenxin Hu; Jun Zheng; Xiaoliang Pan; Yihan Shao; Ye Mei
Journal:  J Chem Theory Comput       Date:  2021-02-16       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.  Positive allosteric mechanisms of adenosine A1 receptor-mediated analgesia.

Authors:  Christopher J Draper-Joyce; Rebecca Bhola; Jinan Wang; Apurba Bhattarai; Anh T N Nguyen; India Cowie-Kent; Kelly O'Sullivan; Ling Yeong Chia; Hariprasad Venugopal; Celine Valant; David M Thal; Denise Wootten; Nicolas Panel; Jens Carlsson; Macdonald J Christie; Paul J White; Peter Scammells; Lauren T May; Patrick M Sexton; Radostin Danev; Yinglong Miao; Alisa Glukhova; Wendy L Imlach; Arthur Christopoulos
Journal:  Nature       Date:  2021-09-08       Impact factor: 49.962

4.  Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.

Authors:  Takefumi Yamashita; Yuxing Peng; Chris Knight; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2012-12-11       Impact factor: 6.006

5.  BuRNN: Buffer Region Neural Network Approach for Polarizable-Embedding Neural Network/Molecular Mechanics Simulations.

Authors:  Bettina Lier; Peter Poliak; Philipp Marquetand; Julia Westermayr; Chris Oostenbrink
Journal:  J Phys Chem Lett       Date:  2022-04-25       Impact factor: 6.888

6.  The adaptive buffered force QM/MM method in the CP2K and AMBER software packages.

Authors:  Letif Mones; Andrew Jones; Andreas W Götz; Teodoro Laino; Ross C Walker; Ben Leimkuhler; Gábor Csányi; Noam Bernstein
Journal:  J Comput Chem       Date:  2015-02-03       Impact factor: 3.376

7.  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

8.  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

9.  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

Review 10.  From adaptive resolution to molecular dynamics of open systems.

Authors:  Robinson Cortes-Huerto; Matej Praprotnik; Kurt Kremer; Luigi Delle Site
Journal:  Eur Phys J B       Date:  2021-09-23       Impact factor: 1.500

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