The role and perspective of ab initio molecular dynamics in the study of biological systems.
Ab initio molecular dynamics (MD) allows realistic simulations to be performed without adjustable parameters. In recent years, the technique has been used on an increasing number of applications to biochemical systems. Here we describe the principles on which ab initio MD is based. We focus on the most popular implementation, based on density functional theory and plane wave basis set. By a survey of recent applications, we show that despite the current limitations of size and time scale, ab initio MD (and hybrid ab initio MD/MM approaches) can play an important role for the modeling of biological systems. Finally, we provide a perspective for the advancement of methodological approaches which may further expand the scope of ab initio MD in biomolecular modeling.
Carloni
Paolo
P
International School for Advanced Studies (SISSA/ISAS) and Istituto Nazionale per la Fisica della Materia (INFM), via Beirut 4, I-34014, Trieste, Italy.
Rothlisberger
Ursula
U
Parrinello
Michele
M
D000818:Animals; D003198:Computer Simulation; D006801:Humans; D008958:Models, Molecular; D009038:Motion; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D011506:Proteins