Coarse-Grain Simulation A Practical Guide

Written for graduate students, researchers, and professionals in the field of materials modeling, this reference provides a concise description of coarse graining. It reviews a broad range of approaches and methods used in the field and offers hands-on, practical information. Chapters describe what coarse materials are used for, when and how to use them, how to analyze their data, and how to test sanity and reliability. This reference connects the fundamental background and theory of coarse graining to its implementation and use in real-world problems.

Introduction/Background
History of the subject (literature review and historical perspective)
Theoretical/physical background overview
Statistical mechanics
Thermodynamics
Kinetics
Practical considerations
Structural considerations
Energy/force considerations
Thermodynamic considerations
Correlation functions
Force field choice
Martin, Klein, Polymer, etc.
Parameterizaiton of new moieties
Programs of choice
Lamps, Gromacs, NAMD, etc.
Some case studies
Analysis of computations
Structural
Dynamical
Energies
Lipid bilayers and vesicles
Proteins
Polymers
Pro and con of different methods
Advanced topics
Converting between AA->CG->AA
Multiscale methods – running both AA and CG in one simulation