Biomolecular Simulations

Methods and Protocols

Editors:

ISBN: 978-1-62703-016-8 (Print) 978-1-62703-017-5 (Online)

Table of contents (26 protocols)

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  1. Front Matter

    Pages i-xiii

  2. Quantum Mechanics Calculations

    1. Front Matter

      Pages 1-1

    2. No Access

      Book Protocol

      Pages 3-27

      Ab Initio, Density Functional Theory, and Semi-Empirical Calculations

    3. No Access

      Book Protocol

      Pages 29-42

      Ab Initio Molecular Dynamics

    4. No Access

      Book Protocol

      Pages 43-66

      Introduction to QM/MM Simulations

    5. No Access

      Book Protocol

      Pages 67-89

      Computational Enzymology

    6. No Access

      Book Protocol

      Pages 91-124

      QM and QM/MM Simulations of Proteins

  3. Classical Mechanics: Atomistic Simulations

    1. Front Matter

      Pages 125-125

    2. No Access

      Book Protocol

      Pages 127-152

      Classical Molecular Dynamics in a Nutshell

    3. No Access

      Book Protocol

      Pages 153-195

      Enhanced Sampling Algorithms

    4. No Access

      Book Protocol

      Pages 197-213

      Force Fields for Classical Molecular Dynamics

    5. No Access

      Book Protocol

      Pages 215-241

      Polarizable Force Fields

    6. No Access

      Book Protocol

      Pages 243-270

      Electrostatics Interactions in Classical Simulations

    7. No Access

      Book Protocol

      Pages 271-311

      An Introduction to Best Practices in Free Energy Calculations

    8. No Access

      Book Protocol

      Pages 313-337

      Recipes for Free Energy Calculations in Biomolecular Systems

    9. No Access

      Book Protocol

      Pages 339-360

      Molecular Docking Methodologies

    10. No Access

      Book Protocol

      Pages 361-405

      Simulation Studies of the Mechanism of Membrane Transporters

    11. No Access

      Book Protocol

      Pages 407-429

      Molecular Dynamics Simulations of Lipid Bilayers: Simple Recipe of How to Do It

    12. No Access

      Book Protocol

      Pages 431-444

      Simulations of Lipid Monolayers

    13. No Access

      Book Protocol

      Pages 445-468

      Simulating DNA by Molecular Dynamics: Aims, Methods, and Validation

    14. No Access

      Book Protocol

      Pages 469-483

      Simulation of Carbohydrates, from Molecular Docking to Dynamics in Water

  4. Mesoscopic Simulations and Coarse-grained Models

    1. Front Matter

      Pages 485-485

    2. No Access

      Book Protocol

      Pages 487-531

      Systematic Methods for Structurally Consistent Coarse-Grained Models

    3. No Access

      Book Protocol

      Pages 533-565

      The Martini Coarse-Grained Force Field

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