Part I: Quantum Mechanics Calculations
1. Ab initio, Density Functional Theory, and Semi-empirical Calculations
Mikael P. Johansson, Ville R. I. Kaila and Dage Sundholm
2. Ab initio Molecular Dynamics
Kari Laasonen
3. Introduction to QM/MM simulations
Gerrit Groenhof
4. Computational Enzymology
Alessio Lodola and Adrian J. Mulholland
5. QM and QM/MM Simulations of Proteins
Thomas Steinbrecher and Marcus Elstner
Part II: Classical Mechanics: Atomistic Simulations
6. Classical Molecular Dynamics in a Nutshell
Susanna Hug
7. Enhanced Sampling Algorithms
Ayori Mitsutake, Yoshiharu Mori, and Yuko Okamoto
8. Force Fields for Classical Molecular Dynamics
Luca Monticelli and D. Peter Tieleman
9. Polarizable Force Fields
Hanne S. Antila and Emppu Salonen
10. Electrostatics interactions in classical simulations
G. Andrés Cisneros, Volodymyr Babin, and Celeste Sagui
11. An Introduction to Best Practices in Free Energy
Calculations
Michael R. Shirts and David L. Mobley
12. Recipes for Free Energy Calculations in Biomolecular Systems
Mahmoud Moradi, Volodymyr Babin, Celeste Sagui, and Christopher Roland
13. Molecular Docking Methodologies
Andrea Bortolato, Marco Fanton, Jonathan S. Mason and Stefano Moro
14. Simulation Studies of the Mechanism of Membrane Transporters
Giray Enkavi, Jing Li, Paween Mahinthichaichan, Po-Chao Wen, Zhijian Huang, Saher A. Shaikh and Emad Tajkhorshid
15. Molecular Dynamics Simulations of Lipid Bilayers: Simple Recipe of How to Do It
Hector Martinez-Seara and Tomasz Róg
16. Simulations of Lipid Monolayers
Svetlana Baoukina and D. Peter Tieleman
17. Simulating DNA by Molecular Dynamics: Aims, Methods, and Validation
Nicolas Foloppe, Marc Guéroult and Brigitte Hartmann
18. Simulation of Carbohydrates, From Molecular Docking to Dynamics in Water
Nicolas Sapay, Alessandra Nurisso and Anne Imberty
Part III: Mesoscopic Simulations and Coarse-grained Models
19. Systematic Methods for Structurally Consistent Coarse-grained
Models
W. G. Noid
20. The Martini Coarse-Grained Force Field
Siewert-Jan Marrink & Xavier Periole
21. Multiscale Molecular Modeling
Matej Praprotnik and Luigi Delle Site
22. Coarse-grained Models for Protein Folding and Aggregation
Philippe Derreumaux
23. Elastic Network Models: Theoretical and Empirical Foundations
Yves-Henri Sanejouand
24. An Introduction to Dissipative Particle Dynamics
Zhong-Yuan Lu, Yong-Lei Wang
25. Multiscale Molecular Dynamics Simulations of Membrane Proteins
Syma Khalid and Peter J Bond
26. Vesicles and Vesicle Fusion: Coarse-grained Simulations
Julian C Shillcock
