A Guide to Biomolecular Simulations

Molecular dynamics simulations have become instrumental in replacing our view of proteins as relatively rigid structures with the realization that they were dynamic systems, whose internal motions play a functional role. Over the years, such simulations have become a central part of biophysics. Appl...

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Bibliographic Details
Main Authors: Becker, Oren M. (Author), Karplus, Martin (Author)
Corporate Author: SpringerLink (Online service)
Format: Electronic eBook
Language:English
Published: Dordrecht : Springer Netherlands, 2006.
Series:Focus on Structural Biology, 4
Subjects:
Online Access:Full Text via HEAL-Link
Table of Contents:
  • Introduction: Note to the Student
  • Introduction: Note to the Instructor
  • Introduction: UNIX
  • Introduction: CHARMM Primer
  • Introduction: CHARMM Template Files
  • Molecular Visualization
  • Energy and Minimization
  • Minimization and Analysis
  • Conformational Analysis
  • Basic Molecular Dynamics in Vacuum and in Solution
  • Molecular Dynamics and Analysis
  • Ligand Dynamics in Myoglobin
  • Normal Mode Analysis
  • Free Energy Calculations
  • Minimum Energy Paths and Transition States
  • Multiple Copy Simultaneous Search
  • Hemoglobin Cooperativity: the T-R Transition.