Biomolecular Simulations

Ab initio, Density Functional Theory, and Semi-empirical Calculations.-Ab initio Molecular Dynamics.-Introduction to QM/MM simulations.-Computational Enzymology.-QM and QM/MM Simulations of Proteins.-Classical Molecular Dynamics in a Nutshell.-Enhanced Sampling Algorithms.-Force Fields for Classical Molecular Dynamics.-Polarizable Force Fields.-Electrostatics Interactions in Classical Simulations.-An Introduction to Best Practices in Free EnergyCalculations.-Recipes for Free Energy Calculations in Biomolecular Systems.-Molecular Docking Methodologies.-Simulation Studies of the Mechanism of Membrane Transporters.-Molecular Dynamics Simulations of Lipid Bilayers: Simple Recipe of How to Do It.-Simulations of Lipid Monolayers.-Simulating DNA by Molecular Dynamics: Aims, Methods, and Validation.-Simulation of Carbohydrates, From Molecular Docking to Dynamics in Water.-Systematic Methods for Structurally Consistent Coarse-grained Models.-The Martini Coarse-Grained Force Field.-Multiscale Molecular Modeling.-Coarse-grained Models for Protein Folding and Aggregation.-Elastic Network Models: Theoretical and Empirical Foundations.-An Introduction to Dissipative Particle Dynamics.-Multiscale Molecular Dynamics Simulations of Membrane Proteins.-Vesicles and Vesicle Fusion: Coarse-grained Simulations.