Ab Initio, density functional theory, and semi-empirical calculations /Mikael P. Johansson, Ville R.I. Kaila, and Dage Sundholm --Ab Initio molecular dynamics /Kari Laasonen --Introduction to QM/MM simulations /Gerrit Groenhof --Computational enzymology /Alessio Lodola and Adrian J. Mulholland --QM and QM/MM simulations of proteins /Thomas Steinbrecher and Marcus Elstner --Classical molecular dynamics in a nutshell /Susanna Hug --Enhanced sampling algorithms /Ayori Mitsutake, Yoshiharu Mori, and Yuko Okamoto --Force fields for classical molecular dynamics /Luca Monticelli and D. Peter Tieleman --Polarizable force fields /Hanne S. Antila and Emppu Salonen --Electrostatics interactions in classical simulations /G. Andres Cisneros, Volodymyr Babin, and Celeste Sagui --Introduction to best practices in free energy calculations /Michael R. Shirts and David L. Mobley --Recipes for free energy calculations in biomolecular systems /Mahmoud Moradi ... [et al.] --Molecular docking methodologies /Andrea Bortolato ... [et al.] --Simulation studies of the mechanism of membrane transporters /Giray Enkavi ... [et al.] --Molecular dynamics simulations of lipid bilayers : simple recipe of how to do it /Hector Martinez-Seara and Tomasz Rog --Simulations of lipid monolayers /Svetlana Baoukina and D. Peter Tieleman --Simulating DNA by molecular dynamics : aims, methods, and validation /Nicolas Foloppe, Marc Gueroult, and Brigitte Hartmann --Simulation of carbohydrates, from molecular docking to dynamics in water /Nicolas Sapay, Alessandra Nurisso, and Anne Imberty --Systematic methods for structurally consistent coarse-grained models /W.G. Noid --Martini coarse-grained force field /Xavier Periole and Siewert-Jan Marrink --Multiscale molecular modeling /Matej Praprotnik and Luigi Delle Site --Coarse-grained models for protein folding and aggregation /Philippe Derreumaux --Elastic network models : theoretical and empirical foundations /Yves-Henri Sanejouand --Introduction to dissipative particle dynamics /Zhong-Yuan Lu and Yong-Lei Wang --Multiscale molecular dynamics simulations of membrane proteins /Syma Khalid and Peter J. Bond --Vesicles and vesicle fusion : coarse-grained simulations /Julian C. Shillcock.