Biomolecular Simulations

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. Andres 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 Rog 16. Simulations of Lipid MonolayersSvetlana Baoukina and D. Peter Tieleman 17. Simulating DNA by Molecular Dynamics: Aims, Methods, and ValidationNicolas Foloppe , Marc Gueroult 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