Bookedited by Luca Monticelli, Emppu Salonen.
Contents:
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 [and others]
Molecular docking methodologies / Andrea Bortolato [and others]
Simulation studies of the mechanism of membrane transporters / Giray Enkavi [and others]
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.