"Molecular dynamics simulations of proteins and peptides: Problems, achievements, and perspectives"Paul Tavan, Heiko Carstens, and Gerald Mathias
In: Protein Folding Handbook. Part I. J. Buchner and T. Kiefhaber (Eds.), Wiley-VCH, Weinheim (2005), 1170-1195.
Starting with a sketch of the basic physics of protein structure and dynamics, Chapter 33 of the Handbook analyzes the state of the art concerning molcular dynamics (MD) simulations based on molecular mechanics (MM) force fields. Major issues are the problems posed by the long range of the electrostatic interactions and by the electronic polarizability commonly neglected in MM force fields.As an example results of MD simulations on light-switchable peptides are discussed.
BMO authors (in alphabetic order):
Long-range electrostatics in molecular dynamics simulations
Polarizable force fields for molecular mechanics from first principles
Photoswitchable model peptides and their conformational dynamics