Guide to Biomolecular Simulations

• 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.

From the reviews:"The Guide to Biomolecular Simulations intends to provide students and nonexperts with an introductory, self-contained course about the application of molecular dynamics and related methodologies. The book emerged from a biophysics course held at Harvard in the 1990s and is therefore suited for standalone self-study as well as for classroom use … . And finally, a reader who successfully worked through the book obtained significant experience in using CHARMM, one of the most widely used molecular dynamics packages in biomolecular simulations." (Anselm H. C. Horn, Journal of Chemical Information and Modeling, Vol. 46 (6), 2006)