Journal ArticleDOI
Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties
Marcus Elstner,Marcus Elstner,D. Porezag,G. Jungnickel,J. Elsner,M. Haugk,Th. Frauenheim,Sándor Suhai,Gotthard Seifert +8 more
TLDR
In this paper, an extension of the tight-binding (TB) approach to improve total energies, forces, and transferability is presented. The method is based on a second-order expansion of the Kohn-Sham total energy in density-functional theory (DFT) with respect to charge density fluctuations.Abstract:
We outline details about an extension of the tight-binding (TB) approach to improve total energies, forces, and transferability. The method is based on a second-order expansion of the Kohn-Sham total energy in density-functional theory (DFT) with respect to charge density fluctuations. The zeroth order approach is equivalent to a common standard non-self-consistent (TB) scheme, while at second order a transparent, parameter-free, and readily calculable expression for generalized Hamiltonian matrix elements may be derived. These are modified by a self-consistent redistribution of Mulliken charges (SCC). Besides the usual ``band structure'' and short-range repulsive terms the final approximate Kohn-Sham energy additionally includes a Coulomb interaction between charge fluctuations. At large distances this accounts for long-range electrostatic forces between two point charges and approximately includes self-interaction contributions of a given atom if the charges are located at one and the same atom. We apply the new SCC scheme to problems where deficiencies within the non-SCC standard TB approach become obvious. We thus considerably improve transferability.read more
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Journal ArticleDOI
CHARMM: the biomolecular simulation program.
Bernard R. Brooks,Charles L. Brooks,Alexander D. MacKerell,Lennart Nilsson,Robert J. Petrella,Benoît Roux,Youngdo Won,Georgios Archontis,Christian Bartels,Stefan Boresch,Amedeo Caflisch,Leo S. D. Caves,Qiang Cui,Aaron R. Dinner,Michael Feig,Stefan Fischer,Jiali Gao,Milan Hodošček,Wonpil Im,K. Kuczera,Themis Lazaridis,Jianpeng Ma,V. Ovchinnikov,Emanuele Paci,Richard W. Pastor,Carol Beth Post,Jingzhi Pu,M. Schaefer,Bruce Tidor,Richard M. Venable,H. L. Woodcock,Xiongwu Wu,Wei Yang,Darrin M. York,Martin Karplus,Martin Karplus +35 more
TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
Book
Electronic Structure: Basic Theory and Practical Methods
TL;DR: In this paper, the Kohn-Sham ansatz is used to solve the problem of determining the electronic structure of atoms, and the three basic methods for determining electronic structure are presented.
Journal ArticleDOI
First-principles calculations for defects and impurities: Applications to III-nitrides
TL;DR: In this paper, the authors describe the state-of-the-art computational methodology for calculating the structure and energetics of point defects and impurities in semiconductors and pay particular attention to computational aspects which are unique to defects or impurities, such as how to deal with charge states and how to describe and interpret transition levels.
Journal ArticleDOI
The Atomic Simulation Environment - A Python library for working with atoms
Ask Hjorth Larsen,Ask Hjorth Larsen,Jens Jørgen Mortensen,Jakob Blomqvist,Ivano E. Castelli,Rune Christensen,Marcin Dulak,Jesper Friis,Michael N. Groves,Bjørk Hammer,Cory Hargus,Eric D. Hermes,Paul C. Jennings,Peter Bjerre Jensen,James R. Kermode,John R. Kitchin,Esben L. Kolsbjerg,Joseph Kubal,Kristen Kaasbjerg,Steen Lysgaard,Jon Bergmann Maronsson,Tristan Maxson,Thomas Olsen,Lars Pastewka,Andrew A. Peterson,Carsten Rostgaard,Jakob Schiøtz,Ole Schütt,Mikkel Strange,Kristian Sommer Thygesen,Tejs Vegge,Lasse B. Vilhelmsen,Michael Walter,Zhenhua Zeng,Karsten Wedel Jacobsen +34 more
TL;DR: The atomic simulation environment (ASE) provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.
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.