Biomolecular simulations : methods and protocols / edited by Luca Monticelli, Emppu Salonen. — New York : Humana Press ; Springer, c2012. – (58.17/M592/v.924) |
Contents
Contents
Preface
Contributors
PART I QUANTUM MECHANICS CALCULATIONS
1 Ab Initio, Density Functional Theory, and Semi-Empirical Calculations
2 Ab Initio Molecular Dynamics
3 Introduction to QM/MM Simulations
4 Computational Enzymology
5 QM and QM/MM Simulations of Proteins
PART II CLASSICAL MECHANICS: ATOMISTIC SIMULATIONS
6 Classical Molecular Dynamics in a Nutshell
7 Enhanced Sampling Algorithms 153
8 Force Fields for Classical Molecular Dynamics
9 Polarizable Force Fields
10 Electrostatics Interactions in Classical Simulations 243
11 An Introduction to Best Practices in Free Energy Calculations 271
12 Recipes for Free Energy Calculations in Biomolecular Systems
13 Molecular Docking Methodologies 339
14 Simulation Studies of the Mechanism of Membrane Transporters 361
15 Molecular Dynamics Simulations of Lipid Bilayers: Simple Recipe of How to Do It 407
16 Simulations of Lipid Monolayers
17 Simulating DNA by Molecular Dynamics: Aims, Methods, and Validation
18 Simulation of Carbohydrates, from Molecular Docking to Dynamics in Water
PART III MESOSCOPIC SIMULATIONS AND COARSE-GRAINED MODELS
19 Systematic Methods for Structurally Consistent Coarse-Grained Models 487
20 The Martini Coarse-Grained Force Field.
21 Multiscale Molecular Modeling
22 Coarse-Grained Models for Protein Folding and Aggregation
23 Elastic Network Models: Theoretical and Empirical Foundations
24 An Introduction to Dissipative Particle Dynamics
25 Multiscale Molecular Dynamics Simulations of Membrane Proteins
26 Vesicles and Vesicle Fusion: Coarse-Grained Simulations