Paper Citing NAMD - Abstract
Zhu, Xiao; Lopes, Pedro E. M.; MacKerell, Alexander D., Jr.
Recent developments and applications of the CHARMM force fields
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 2:167-185, JAN-FEB 2012
Empirical force fields (FFs) commonly used to describe the condensed-phase properties of complex systems such as biological macromolecules are continuously being updated. Improvements in quantum mechanical methods used to generate target data, availability of new experimental target data, incorporation of new classes of compounds, and new theoretical developments (e.g., polarizable methods) make FF development a dynamic domain of research. Accordingly, a number of improvements and extensions of the Chemistry at HARvard Molecular Mechanics (CHARMM) FFs have occurred over the years. The objective of the present review is to provide an up-to-date overview of the CHARMM FFs. A limited presentation on the historical aspects of FFs will be given, including underlying methodologies and principles, along with a brief description of the strategies used for parameter development. This is followed by information on the CHARMM additive and polarizable FFs, including examples of recent applications of those FFs. (c) 2011 John Wiley & Sons, Ltd.
