Paper Citing NAMD - Abstract
Emperador, Agusti; Carrillo, Oliver; Rueda, Manuel; Orozco, Modesto
Exploring the suitability of coarse-grained techniques for the representation of protein dynamics
BIOPHYSICAL JOURNAL, 95:2127-2138, SEP 1 2008
A systematic study of two coarse-grained techniques for the description of protein dynamics is presented. The two techniques exploit either Brownian or discrete molecular dynamics algorithms applied in the context of simple C-alpha-C-alpha potentials, like those used in coarse-grained normal mode analysis. Coarse-grained simulations of the flexibility of protein metafolds are compared to those computed with fully atomistic molecular dynamics simulations using state-of-the-art physical potentials and explicit solvent. Both coarse-grained models efficiently capture critical features of the protein dynamics.
