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      Interfacing the Core-Shell or the Drude Polarizable Force Field With Car–Parrinello Molecular Dynamics for QM/MM Simulations

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      Frontiers in Chemistry
      Frontiers Media S.A.
      QMMM simulations, MD, POLARIZED MM, catalysis, CPMD-GULP

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          Abstract

          We report a quantum mechanics/polarizable–molecular mechanics (QM/p–MM) potential based molecular dynamics (MD) technique where the core–shell (or the Drude) type polarizable MM force field is interfaced with the plane-wave density functional theory based QM force field which allows Car–Parrinello MD for the QM subsystem. In the QM/p-MM Lagrangian proposed here, the shell (or the Drude) MM variables are treated as extended degrees of freedom along with the Kohn–Sham (KS) orbitals describing the QM wavefunction. The shell and the KS orbital degrees of freedom are then adiabatically decoupled from the nuclear degrees of freedom. In this respect, we also present here the Nosé–Hoover Chain thermostat implementation for the dynamical subsystems. Our approach is then used to investigate the effect of MM polarization on the QM/MM results. Especially, the consequence of MM polarization on reaction free energy barriers, defect formation energy, and structural and dynamical properties are investigated. A low point charge polarizable potential (p–MZHB) for pure siliceous systems is also reported here.

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          Generalized Gradient Approximation Made Simple.

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            Nosé–Hoover chains: The canonical ensemble via continuous dynamics

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              Escaping free-energy minima

              We introduce a novel and powerful method for exploring the properties of the multidimensional free energy surfaces of complex many-body systems by means of a coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates.A characteristic feature of this dynamics is the presence of a history-dependent potential term that, in time, fills the minima in the free energy surface, allowing the efficient exploration and accurate determination of the free energy surface as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissociation of a NaCl molecule in water and in the study of the conformational changes of a dialanine in solution.
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                Author and article information

                Contributors
                Journal
                Front Chem
                Front Chem
                Front. Chem.
                Frontiers in Chemistry
                Frontiers Media S.A.
                2296-2646
                10 July 2018
                2018
                : 6
                : 275
                Affiliations
                Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur, India
                Author notes

                Edited by: Sam P. De Visser, University of Manchester, United Kingdom

                Reviewed by: Thomas S. Hofer, University of Innsbruck, Austria; Hugo Gattuso, University of Liége, Belgium

                *Correspondence: Nisanth N. Nair nnair@ 123456iitk.ac.in

                This article was submitted to Theoretical and Computational Chemistry, a section of the journal Frontiers in Chemistry

                †Present Address: Sudhir K. Sahoo, Department Chemie, Universität Paderborn, Paderborn, Germany

                Article
                10.3389/fchem.2018.00275
                6048201
                17b65ef4-f2e8-4050-83ec-dcca8c1bd61f
                Copyright © 2018 Sahoo and Nair.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 22 February 2018
                : 18 June 2018
                Page count
                Figures: 7, Tables: 4, Equations: 16, References: 52, Pages: 10, Words: 6189
                Funding
                Funded by: Education, Audiovisual and Culture Executive Agency 10.13039/501100000785
                Award ID: 557100-EPP-1-2014-1-EL-SPO-SCP
                Categories
                Chemistry
                Original Research

                qmmm simulations,md,polarized mm,catalysis,cpmd-gulp
                qmmm simulations, md, polarized mm, catalysis, cpmd-gulp

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