Book Volume 4 2006

A Guide to Biomolecular Simulations

Authors:

ISBN: 978-1-4020-3586-9 (Print) 978-1-4020-3587-6 (Online)

Table of contents (17 chapters)

  1. Front Matter

    Pages i-ix

  2. No Access

    Chapter

    Pages 1-2

    Introduction: Note to the Student

  3. No Access

    Chapter

    Pages 3-3

    Introduction: Note to the Instructor

  4. No Access

    Chapter

    Pages 4-9

    Introduction: UNIX

  5. No Access

    Chapter

    Pages 10-17

    Introduction: CHARMM Primer

  6. No Access

    Chapter

    Pages 18-18

    Introduction: CHARMM Template Files

  7. No Access

    Chapter

    Pages 19-33

    Molecular Visualization

  8. No Access

    Chapter

    Pages 35-50

    Energy and Minimization

  9. No Access

    Chapter

    Pages 51-63

    Minimization and Analysis

  10. No Access

    Chapter

    Pages 65-74

    Conformational Analysis

  11. No Access

    Chapter

    Pages 75-99

    Basic Molecular Dynamics in Vacuum and in Solution

  12. No Access

    Chapter

    Pages 101-130

    Molecular Dynamics and Analysis

  13. No Access

    Chapter

    Pages 131-154

    Ligand Dynamics in Myoglobin

  14. No Access

    Chapter

    Pages 155-171

    Normal Mode Analysis

  15. No Access

    Chapter

    Pages 173-192

    Free Energy Calculations

  16. No Access

    Chapter

    Pages 193-203

    Minimum Energy Paths and Transition States

  17. No Access

    Chapter

    Pages 205-212

    Multiple Copy Simultaneous Search

  18. No Access

    Chapter

    Pages 213-220

    Hemoglobin Cooperativity: the T-R Transition

  19. Back Matter

    Pages 221-221