Paper Citing NAMD - Abstract
Luitz, Manuel; Bomblies, Rainer; Ostermeir, Katja; Zacharias, Martin
Exploring biomolecular dynamics and interactions using advanced sampling methods
JOURNAL OF PHYSICS-CONDENSED MATTER, 27 Art. No. 323101, AUG 19 2015
Molecular dynamics (MD) and Monte Carlo (MC) simulations have emerged as a valuable tool to investigate statistical mechanics and kinetics of biomolecules and synthetic soft matter materials. However, major limitations for routine applications are due to the accuracy of the molecular mechanics force field and due to the maximum simulation time that can be achieved in current simulations studies. For improving the sampling a number of advanced sampling approaches have been designed in recent years. In particular, variants of the parallel tempering replica-exchange methodology are widely used in many simulation studies. Recent methodological advancements and a discussion of specific aims and advantages are given. This includes improved free energy simulation approaches and conformational search applications.
