Journal ArticleDOI
A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations
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In this article, a fully Hamiltonian and computationally efficient scheme to include the electrostatic effects due to the classical environment in a Car-Parrinello mixed quantum mechanics/molecular mechanics (QM/MM) method is presented.Abstract:
We present a fully Hamiltonian and computationally efficient scheme to include the electrostatic effects due to the classical environment in a Car–Parrinello mixed quantum Mechanics/molecular mechanics (QM/MM) method. The polarization due to the MM atoms close to the quantum system is described by a Coulombic potential modified at short range. We show that the functional form of this potential has to be chosen carefully in order to obtain the correct interaction properties and to prevent an unphysical escape of the electronic density to the MM atoms (the so-called spill-out effect). The interaction between the QM system and the more distant MM atoms is modeled by a Hamiltonian term explicitly coupling the multipole moments of the quantum charge distribution with the classical point charges. Our approach remedies some of the well known deficiencies of current electrostatic coupling schemes in QM/MM methods, allowing molecular dynamics simulations of mixed systems within a fully consistent and energy conser...read more
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Journal ArticleDOI
Quantum mechanical continuum solvation models.
TL;DR: This paper presents a meta-modelling procedure called "Continuum Methods within MD and MC Simulations 3072", which automates the very labor-intensive and therefore time-heavy and expensive process of integrating discrete and continuous components into a discrete-time model.
Journal ArticleDOI
Advanced capabilities for materials modelling with Quantum ESPRESSO.
Paolo Giannozzi,Oliviero Andreussi,Oliviero Andreussi,Thomas Brumme,Oana Bunau,M. Buongiorno Nardelli,Matteo Calandra,Roberto Car,Carlo Cavazzoni,Davide Ceresoli,Matteo Cococcioni,Nicola Colonna,Ivan Carnimeo,A. Dal Corso,S. de Gironcoli,Pietro Delugas,Robert A. DiStasio,Andrea Ferretti,Andrea Floris,Guido Fratesi,Giorgia Fugallo,Ralph Gebauer,Uwe Gerstmann,Feliciano Giustino,Tommaso Gorni,Tommaso Gorni,Junteng Jia,Mitsuaki Kawamura,Hsin-Yu Ko,Anton Kokalj,Emine Kucukbenli,Michele Lazzeri,M. Marsili,Nicola Marzari,Francesco Mauri,Ngoc Linh Nguyen,Huy-Viet Nguyen,Alberto Otero-de-la-Roza,Lorenzo Paulatto,Samuel Poncé,Dario Rocca,Dario Rocca,Riccardo Sabatini,Biswajit Santra,Martin Schlipf,Ari P. Seitsonen,Ari P. Seitsonen,Alexander Smogunov,Iurii Timrov,Timo Thonhauser,Paolo Umari,Nathalie Vast,Xifan Wu,Stefano Baroni +53 more
TL;DR: Recent extensions and improvements are described, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.
Journal ArticleDOI
Advanced capabilities for materials modelling with Quantum ESPRESSO
Paolo Giannozzi,Oliviero Andreussi,Oliviero Andreussi,Thomas Brumme,Oana Bunau,M. Buongiorno Nardelli,Matteo Calandra,Roberto Car,Carlo Cavazzoni,Davide Ceresoli,Matteo Cococcioni,Nicola Colonna,Ivan Carnimeo,A. Dal Corso,S. de Gironcoli,Pietro Delugas,Robert A. DiStasio,Andrea Ferretti,Andrea Floris,Guido Fratesi,Giorgia Fugallo,Ralph Gebauer,Uwe Gerstmann,Feliciano Giustino,Tommaso Gorni,Tommaso Gorni,Junteng Jia,Mitsuaki Kawamura,Hsin-Yu Ko,Anton Kokalj,Emine Kucukbenli,Michele Lazzeri,M. Marsili,Nicola Marzari,Francesco Mauri,Ngoc Linh Nguyen,Huy-Viet Nguyen,Alberto Otero-de-la-Roza,Lorenzo Paulatto,Samuel Poncé,Dario Rocca,Dario Rocca,Riccardo Sabatini,Biswajit Santra,Martin Schlipf,Ari P. Seitsonen,Ari P. Seitsonen,Alexander Smogunov,Iurii Timrov,Timo Thonhauser,Paolo Umari,Nathalie Vast,Xifan Wu,Stefano Baroni +53 more
TL;DR: Quantum ESPRESSO as discussed by the authors is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density functional theory, density functional perturbation theory, and many-body perturbations theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches.
Journal ArticleDOI
QM/MM Methods for Biomolecular Systems
Hans Martin Senn,Walter Thiel +1 more
TL;DR: To model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region and an MM treatment for the surroundings, enabling the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.
Journal ArticleDOI
QM/MM: what have we learned, where are we, and where do we go from here?
TL;DR: A review of the most popular methods for combined quantum mechanical/molecular mechanical (QM/MM) calculations, including their advantages and disadvantages, can be found in this article.
References
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Journal ArticleDOI
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
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