# *Ab Initio* Molecular Dynamics: Basic Theory and Advanced Methods

Blurb cited from the back of the book:

“Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and electronic structure theory. This book provides the first coherent presentation of this rapidly growing field, covering a vast range of methods and their applications, from basic theory to advanced methods. This fascinating text for graduate students and researchers contains systematic derivations of various ab initio molecular dynamics techniques to enable readers to understand and assess the merits and drawbacks of commonly used methods. It also discusses the special features of the widely used Car-Parrinello approach, correcting various misconceptions currently found in the research literature. The book contains pseudo-code and program layout for typical plane wave electronic structure codes, allowing newcomers to the field to understand commonly used program packages, and enabling developers to improve and add new features in their code.”

This monograph should be cited as follows:

D. Marx and J. Hutter,

* Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods, *

(Cambridge University Press, Cambridge 2009)

ISBN: 978–0–521–89863–8, hardback, 578 pages, 1669 references

- CUP Homepage of the book:
*http://www.cambridge.org/9780521898638* *Look inside the book: click here!*- Errata and Addenda of the book: click here!

# Computational Trends in Solvation and Transport in Liquids

The present Jülich CECAM School on Computational Science, which is co-supported by the Cluster of Excellence Ruhr Explores Solvation RESOLV, has a main focus on “Solvation Science”, which is increasingly recognized as an interdisciplinary field akin to “Materials Science” or “Neuroscience”. The School addresses a variety of different computational and simulation methods, appropriate for those hierarchies of time- and length-scales which are a challenge for modeling and simulation in Solvation Science. Therefore, the School is intended as a continuation of former Schools, organized in Jülich in 2009 and 2012, focusing on Multiscale Simulation Methods in Molecular Sciences and Hierarchical Methods for Dynamics in Complex Molecular Systems. The key of the present School is to introduce to a broad scientific audience modern computational methods which originate from a wide background but which can be applied to a variety of different scales, both in time and length, to describe solvation and transport phenomena on different levels of approximation. Problems associated with solvation and transport emerge in various distinct fields, ranging from fundamental questions in wet chemistry or soft matter physics to industrial applications in chemical engineering, which naturally induces a highly interdisciplinary character. Therefore, one aim of this School is to bring people together from diverse disciplines and various background in addition to triggering exchange of ideas between established experts and students—being the next generation of researchers.

This book should be cited as follows:

G. Sutmann, J. Grotendorst, G. Gompper, and D. Marx,

“Computational Trends in Solvation and Transport in Liquids” (Forschungszentrum Jülich 2015)

# Hierarchial Methods for Dynamics in Complex Molecular Systems

Generating and analyzing the dynamics of molecular systems is a true challenge to molecular simulation. It includes processes that happen on the femtosecond scale, such as photoinduced nonadiabatic (bio)chemical reactions, and touches the range of seconds, being e.g. relevant in biophysics to cellular processes or in material sciences to crack propagation. Thus, many orders of magnitude in time need to be covered either concurrently or hierarchically. The key issue of this book is to dwell on hierarchical methods for dynamics having primarily in mind systems described in terms of many atoms or molecules. One extreme end of relevant time scales is found in the sub-femtosecond range but which influence dynamical events which are orders of magnitude slower. Examples for such phenomena might be photo-induced switching of individual molecules, which results in large-amplitude relaxation in liquids or photodriven phase transitions of liquid crystals, phenomena for which nonadiabatic quantum dynamics methods were developed. The other end of relevant time scales is found in a broad range of microseconds, seconds or beyond and which governs e.g. non-equilibrium dynamics in polymer flows or blood cells in complex geometries like microvessels. Special mesoscopic techniques are applied for these time- and length-scales to couple the atomistic nature of particles to the hydrodynamics of flows.

This book should be cited as follows:

J. Grotendorst, G. Sutmann, G. Gompper, and D. Marx,

“Hierarchial Methods for Dynamics in Complex Molecular Systems” (Forschungszentrum Jülich 2012)

# Multiscale Simulation Methods in Molecular Sciences

In this book, three topic areas will be covered focusing on how to deal with hard matter, soft matter, and bio matter where it is necessary to cope with disparate length and time scales. Aspects like coarse graining of molecular systems and solids, quantum/classical hybrid methods, embedding and multiple time step techniques, creating reactive potentials, multiscale magnetism, adaptive resolution ideas or hydrodynamic interactions will be discussed in detail. In addition, another series of lectures will be devoted to the genuine mathematical and the generic algorithmic aspects of multiscale approaches and their parallel implementation on large, multiprocessor platforms including techniques such as multigrid and wavelet transformations. Although this is beyond what can be achieved in a very systematic fashion given the breadth of the topic, introductions will be given to fundamental techniques such as molecular dynamics, Monte Carlo simulation, and electronic structure (total energy) calculations in the flavour of both wavefunction-based and density-based methods.

This book should be cited as follows:

J. Grotendorst, N. Attig, S. Blügel, and D. Marx,

“Multiscale Simulation Methods in Molecular Sciences” (Forschungszentrum Jülich 2009)

# Computational Nanoscience: Do It Yourself!

NIC Winter School 2006: Computational science plays an ever increasing role in understanding materials and molecular systems. The nanometer scale in particular is governed by the laws of quantum mechanics, which calls for electronic structure theory in order to address questions related to stability of structures, chemical processes or spectral properties. This hands-on NIC Winter School focuses on the application of modern electronic structure calculations and dynamical simulation techniques covering aspects of solid state and surface science, chemical reactions and dynamics, as well as the structure and properties of large molecules and clusters. The School will provide a practical introduction to the theory behind and handling of pertinent software packages through practicals and tutorials in small groups using four codes. The full-potential linearized augmented plane wave code FLEUR and the Korringa-Kohn-Rostocker Green function code KKR-GF, the ab initio (Car-Parrinello) molecular dynamics simulation package CPMD, and the highly efficient quantum chemistry code TURBOMOLE. Although very different in concept and application focus, all these codes are well-known prototypical representatives and are used in various supercomputer centres around the world.

The Lecture Notes can be downloaded for free (as an alternative to ordering a nice hardbound version from the NIC Secretariat).

This book should be cited as follows:

J. Grotendorst, S. Blügel, and D. Marx,

“Computational Nanoscience: Do It Yourself!” (NIC, FZ Jülich 2006)

# Parrinello Festschrift: From Physics via Chemistry to Biology

From the Editorial: It is an honor and a pleasure to dedicate this *Festschrift* to Professor Michele Parrinello on the occasion of his 60th birthday. His various original contributions to modern computational methods and algorithms in the realm of molecular sciences are invaluable and we are confident that they will enjoy an ever growing impact on our understanding thereof. Indeed, his work has already opened many new avenues for the study of processes and properties in diverse fields ranging from liquids to chemical reactions and biochemistry, bridging the gap from fundamental methodology to groundbreaking applications. It is instructive to retrace Parrinello's path in science, from...

The Editorial should be cited as follows:

W. Andreoni, D. Marx, and M. Sprik,

*A Tribute to Michele Parrinello: From Physics via Chemistry to Biology* (Editorial of the “Parrinello Festschrift”),

ChemPhysChem **6**, p. 1671–1676 (2005).

The *Festschrift* should be cited as follows:

W. Andreoni, D. Marx, and M. Sprik,

*Parrinello Festschrift: From Physics via Chemistry to Biology* (Special Issue),

ChemPhysChem Volume **6**, p. 1671–1947 (2005).

Note: it is illegal to download these PDF files: please contact us at theochem@theochem.rub.de and you will receive a legal reprint as soon as possible.

# Theoretical Chemistry in the 21st Century: The ‘Virtual Lab’

Electronic structure calculation and computer simulation became unified by Car and Parrinello in terms of a dynamical propagation scheme where the orbitals are treated as fictitious scalar fields obeying classical mechanics. This allows the treatment of multicomponent systems with complicated interactions based on first principles. Most importantly within Chemistry, this idea opens an avenue to studying chemical reactions that involve many coupled degrees of freedom, such as those taking place in liquids, in the computer. It is argued that one important branch of Theoretical Chemistry will be devoted to developing and applying such “virtual laboratory methods”. Two recent examples where chemical reactions are induced by photons (photochemistry) or by an external mechanical force (mechanochemistry) are presented. The article can be downloaded as a PDF file.

This article should be cited as follows:

D. Marx,

Theoretical Chemistry in the 21st Century: The ‘Virtual Lab’,

in “Proceedings of the Idea-Finding Symposium: Frankfurt Institute for Advanced Studies” (p. 139–153),

Editors: W. Greiner and J. Reinhardt,

(EP Systema, Debrecen, 2004).

# Quantum Simulations of Complex Many-Body Systems: From Theory to Algorithms

For a broader overview about the state-of-the-art quantum simulation techniques in general see the Lecture Notes of the NIC 2002 Winter School on Quantum Simulations which you can download for free (as an alternative to ordering a nice hardbound version from the NIC Secretariat).

This book should be cited as follows:

J. Grotendorst, D. Marx, and A. Muramatsu, “Quantum Simulations of Complex Many-Body Systems: From Theory to Algorithms” (NIC, FZ Jülich 2002)

In addition, an audio-visual multimedia presentation of the entire NIC 2002 Winter School is available on the web (the corresponding DVD can also be ordered from the NIC Secretariat).

# First Principles Molecular Dynamics Involving Excited States and Nonadiabatic Transitions

Extensions of traditional molecular dynamics to excited electronic states and non-Born-Oppenheimer dynamics are reviewed focussing on applicability to chemical reactions of large molecules, possibly in condensed phases. The review exclusively deals with *ab initio* “on the fly” molecular dynamics methods.

Note: It is illegal to download this PDF file: please contact us at theochem@theochem.rub.de and you will receive a legal reprint of this article as soon as possible.

This article should be cited as follows:

N. L. Doltsinis and D. Marx,

“First Principles Molecular Dynamics Involving Excited States and Nonadiabatic Transitions”,

J. Theor. Comput. Chem. **1**, 319–349 (2002).

*Ab Initio* Molecular Dynamics: Theory and Implementation

This review article describes various types of *ab initio* molecular dynamics techniques (such as e.g. Car-Parrinello molecular dynamics) and the particular implementation of these methods in the `CPMD code`. In addition, lots of references to applications in various fields are compiled. The article can be downloaded as a PDF or as a Postscript file.

This article should be cited as follows:

D. Marx and J. Hutter,

“*Ab Initio* Molecular Dynamics: Theory and Implementation”,

in “Modern Methods and Algorithms of Quantum Chemistry” (p. 301–449),

Editor: J. Grotendorst,

(NIC, FZ Jülich 2000).