As computational hardware continues to develop at a rapid pace, quantitative computations are playing an increasingly essential role in the study of biomolecular systems. One of the most important challenges that the field faces is to develop the next generation of computational models that strike the proper balance of computational efficiency and accuracy, so that the problems of increasing complexity can be tackled in a systematic and physically robust manner. In particular, properly treating intermolecular interactions is fundamentally important for the reliability of all computational models. In this book, contributions by leading experts in the area of biomolecular simulations discuss cutting-edge ideas regarding effective strategies to describe many-body effects and electrostatics at quantum, classical, and coarse-grained levels. The goal of the book is to not only provide an up-to-date snapshot of the current simulation field but also stimulate exchange of ideas across different sub-fields of modern computational (bio)chemistry. The text will be a useful reference for the biomolecular simulation community and help attract talented young students into this exciting frontier of research.
QM and QM/MM Methods
Polarizable continuum models for (bio)molecular electrostatics: Basic theory and recent developments for macromolecules and simulations, J. M. Herbert, A. W. Lange
A modified divide-and-conquer linear-scaling quantum force field with multipolar charge densities, T. J. Giese, D. M. York
Explicit polarization theory, Y. Wang, M. J. M. Mazack, D. G. Truhlar, J. Gao
Effective fragment potential method, L. Slipchenko
Quantum mechanical methods for quantifying and analyzing non-covalent interactions and for force-field development, D. Sherrill, K. Merz
Force field development with density-based energy decomposition analysis, N. Zhou, Q. Wu, Y. Zhang
Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: a review, W. Guowei, N. Baker
Explicit inclusion of induced polarization in atomistic force fields based on the classical Drude oscillator model, A. Savelyev, B. Roux, A. D. Mackerell, Jr.
Multipolar force fields for atomistic simulations, M. Meuwly, T. Bereau
Quantum mechanics based polarizable force field for proteins, C. Ji, Y. Mei, J. Zhang
Status of the Gaussian electrostatic model, a density-based polarizable force field, G. A. Cisneros, J.-P. Piquemal
Water models: Looking forward by looking backward, T. Ichiye
A physics-based coarse-grained model with electric multipoles, G. Li
Coarse-grained membrane force field based on Gay–Berne potential and electric multipoles, D. Lin, A. Grossfield
Perspectives on the coarse-grained models of DNA, I. Echeverria, G. Papoian
RNA coarse-grained model theory, D. Bell, P. Ren
"This book is a state-of-the-art report on the description of molecular energetics using force fields, which are the most critical element in computer simulations of biomolecular systems. The 16 chapters, written by leaders in the field, provide in-depth reports on all important current issues, including the representation of polarization, quantum mechanics-based force fields, and coarse-grained approaches for RNA, DNA, and membranes. This is an important reference for anyone involved in computational studies in chemistry and biology, especially those who want a deeper understanding of the underlying representations of intra- and intermolecular energetics."
—Prof. William L. Jorgensen, Yale University, USA