Paper Citing NAMD - Abstract
Bellucci, L.; Brancolini, G.; Calzolari, A.; Parramon, O. Carrillo; Corni, S.; Di Felice, R.
Proteins and Peptides at Gold Surfaces: Insights from Atomistic Simulations
PROTEINS AT INTERFACES III: STATE OF THE ART, 1120:229-250, 2012
Computer simulations at the atomistic level, jointly with experiments, can provide the microscopic picture behind protein-surface interactions. The complexity of the inherent phenomena, that span several time and length scales, call for a hierarchical strategy, from electronic structure approaches (limited in the accessible sizes and times) to classical methods, able to treat larger systems and longer time scales, but involving more assumptions and providing less details. Here we introduce the atomistic simulation methods that we have developed and applied to treat the interaction of peptides and proteins with the Au(111) surface in water. We succinctly describe principles, assumptions and limitations of ab initio, classical atomistic molecular dynamics and Brownian dynamics docking methods as applied to the protein-surface problem, with specific focus on the work of our group. The possible extension to coarse-grained method is also discussed.
