Over the past 40 years the field of molecular simulations has evolved from picosecond studies of isolated macromolecules in vacuum to studies of complex, chemically heterogeneous biological systems consisting of millions of atoms, with the simulation time scales spanning up to milliseconds. In Biomolecular Simulations: Methods and Protocols, expert researchers illustrate many of the methods commonly used in molecular modelling of biological systems, including methods for electronic structure calculations, classical molecular dynamics simulations and coarse-grained techniques. A selection of advanced techniques and recent methodological developments, which rarely find coverage in traditional textbooks, is also introduced.
 
Written in the highly successful Methods in Molecular Biology series format, chapters include general introductions to well-established computational methodologies, applications to real-world biological systems, as well as practical tips and general protocols on carrying out biomolecular simulations. Special emphasis is placed on simulations of proteins, lipids, nucleic acids, and carbohydrates. Authoritative and practical, Biomolecular Simulations: Methods and Protocols seeks to aid scientists in further simulation studies of biological systems.

Part I: Quantum Mechanics Calculations1. Ab initio, Density Functional Theory, and Semi-empirical CalculationsMikael P. Johansson, Ville R. I. Kaila and Dage Sundholm 2. Ab initio Molecular DynamicsKari Laasonen 3. Introduction to QM/MM simulationsGerrit Groenhof 4. Computational EnzymologyAlessio Lodola and Adrian J. Mulholland 5. QM and QM/MM Simulations of ProteinsThomas Steinbrecher and Marcus Elstner Part II: Classical Mechanics: Atomistic Simulations  6. Classical Molecular Dynamics in a NutshellSusanna Hug 7. Enhanced Sampling AlgorithmsAyori Mitsutake, Yoshiharu Mori, and Yuko Okamoto 8. Force Fields for Classical Molecular DynamicsLuca Monticelli  and D. Peter Tieleman 9. Polarizable Force FieldsHanne S. Antila and Emppu Salonen 10. Electrostatics interactions in classical simulationsG. Andrés Cisneros, Volodymyr Babin, and Celeste Sagui 11. An Introduction to Best Practices in Free EnergyCalculationsMichael R. Shirts  and David L. Mobley 12. Recipes for Free Energy Calculations in Biomolecular SystemsMahmoud Moradi, Volodymyr Babin, Celeste Sagui, and Christopher Roland 13. Molecular Docking MethodologiesAndrea Bortolato, Marco Fanton, Jonathan S. Mason and Stefano Moro 14. Simulation Studies of the Mechanism of Membrane TransportersGiray 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 ItHector Martinez-Seara and Tomasz Róg 16. Simulations of Lipid MonolayersSvetlana Baoukina and D. Peter Tieleman 17. Simulating DNA by Molecular Dynamics: Aims, Methods, and ValidationNicolas Foloppe , Marc Guéroult and Brigitte Hartmann  18. Simulation of Carbohydrates, From Molecular Docking to Dynamics in WaterNicolas Sapay, Alessandra Nurisso and Anne Imberty   Part III: Mesoscopic Simulations and Coarse-grained Models  19. Systematic Methods for Structurally Consistent Coarse-grainedModelsW. G. Noid 20. The Martini Coarse-Grained Force FieldSiewert-Jan Marrink & Xavier Periole 21. Multiscale Molecular ModelingMatej Praprotnik and Luigi Delle Site 22. Coarse-grained Models for Protein Folding and AggregationPhilippe Derreumaux 23. Elastic Network Models: Theoretical and Empirical FoundationsYves-Henri Sanejouand 24. An Introduction to Dissipative Particle DynamicsZhong-Yuan Lu, Yong-Lei Wang 25. Multiscale Molecular Dynamics Simulations of Membrane ProteinsSyma Khalid  and Peter J Bond  26. Vesicles and Vesicle Fusion: Coarse-grained SimulationsJulian C Shillcock