Literature DB >> 25178266

The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties.

Saleh Riahi1, Christopher N Rowley.   

Abstract

The quantum mechanical (QM)/molecular mechanical (MM) interface between Chemistry at HARvard Molecular Mechanics (CHARMM) and TURBOMOLE is described. CHARMM provides an extensive set of simulation algorithms, like molecular dynamics (MD) and free energy perturbation, and support for mature nonpolarizable and Drude polarizable force fields. TURBOMOLE provides fast QM calculations using density functional theory or wave function methods and excited state properties. CHARMM-TURBOMOLE is well-suited for extended QM/MM MD simulations using first principles methods with large (triple-ζ) basis sets. We demonstrate these capabilities with a QM/MM simulation of Mg(2+) (aq), where the MM outer sphere water molecules are represented using the SWM4-NDP Drude polarizable force field and the ion and inner coordination sphere are represented using QM PBE, PBE0, and MP2 methods. The relative solvation free energies of Mg(2+) and Zn(2+) were calculated using thermodynamic integration. We also demonstrate the features for excited state properties. We calculate the time-averaged solution absorption spectrum of indole, the emission spectrum of the indole 1La excited state, and the electronic circular dichroism spectrum of an oxacepham.
Copyright © 2014 Wiley Periodicals, Inc.

Entities:  

Keywords:  CHARMM; TURBOMOLE; electronic absorption spectrum; electronic circular dichroism spectrum; emission spectrum; ion solvation; polarizable force field; quantum mechanical/molecular mechanical

Year:  2014        PMID: 25178266     DOI: 10.1002/jcc.23716

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  26 in total

1.  Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions.

Authors:  Jonah Z Vilseck; Jakub Kostal; Julian Tirado-Rives; William L Jorgensen
Journal:  J Comput Chem       Date:  2015-08-27       Impact factor: 3.376

2.  Polarizable molecular dynamics simulations of ionic liquids: Influence of temperature control.

Authors:  Esther Heid; Stefan Boresch; Christian Schröder
Journal:  J Chem Phys       Date:  2020-03-07       Impact factor: 3.488

3.  Symmetry-related proton transfer pathways in respiratory complex I.

Authors:  Andrea Di Luca; Ana P Gamiz-Hernandez; Ville R I Kaila
Journal:  Proc Natl Acad Sci U S A       Date:  2017-07-17       Impact factor: 11.205

4.  Energetics and dynamics of a light-driven sodium-pumping rhodopsin.

Authors:  Carl-Mikael Suomivuori; Ana P Gamiz-Hernandez; Dage Sundholm; Ville R I Kaila
Journal:  Proc Natl Acad Sci U S A       Date:  2017-06-13       Impact factor: 11.205

5.  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

6.  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

7.  Structural basis of mammalian complex IV inhibition by steroids.

Authors:  Justin M Di Trani; Agnes Moe; Daniel Riepl; Patricia Saura; Ville R I Kaila; Peter Brzezinski; John L Rubinstein
Journal:  Proc Natl Acad Sci U S A       Date:  2022-07-19       Impact factor: 12.779

8.  Electric fields control water-gated proton transfer in cytochrome c oxidase.

Authors:  Patricia Saura; Daniel Riepl; Daniel M Frey; Mårten Wikström; Ville R I Kaila
Journal:  Proc Natl Acad Sci U S A       Date:  2022-09-12       Impact factor: 12.779

9.  TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations.

Authors:  Sree Ganesh Balasubramani; Guo P Chen; Sonia Coriani; Michael Diedenhofen; Marius S Frank; Yannick J Franzke; Filipp Furche; Robin Grotjahn; Michael E Harding; Christof Hättig; Arnim Hellweg; Benjamin Helmich-Paris; Christof Holzer; Uwe Huniar; Martin Kaupp; Alireza Marefat Khah; Sarah Karbalaei Khani; Thomas Müller; Fabian Mack; Brian D Nguyen; Shane M Parker; Eva Perlt; Dmitrij Rappoport; Kevin Reiter; Saswata Roy; Matthias Rückert; Gunnar Schmitz; Marek Sierka; Enrico Tapavicza; David P Tew; Christoph van Wüllen; Vamsee K Voora; Florian Weigend; Artur Wodyński; Jason M Yu
Journal:  J Chem Phys       Date:  2020-05-14       Impact factor: 3.488

10.  A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations.

Authors:  Xiaoliang Pan; Kwangho Nam; Evgeny Epifanovsky; Andrew C Simmonett; Edina Rosta; Yihan Shao
Journal:  J Chem Phys       Date:  2021-01-14       Impact factor: 3.488

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