@article{doi:10.1021/ct300854w,
author = {Jamroz, Michal and Orozco, Modesto and Kolinski, Andrzej and Kmiecik, Sebastian},
title = {Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field},
journal = {Journal of Chemical Theory and Computation},
volume = {9},
number = {1},
pages = {119-125},
year = {2013},
doi = {10.1021/ct300854w},

URL = {http://pubs.acs.org/doi/abs/10.1021/ct300854w},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/ct300854w},
abstract = { It is widely recognized that atomistic Molecular Dynamics (MD), a classical simulation method, captures the essential physics of protein dynamics. That idea is supported by a theoretical study showing that various MD force-fields provide a consensus picture of protein fluctuations in aqueous solution [Rueda, M. et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796–801]. However, atomistic MD cannot be applied to most biologically relevant processes due to its limitation to relatively short time scales. Much longer time scales can be accessed by properly designed coarse-grained models. We demonstrate that the aforementioned consensus view of protein dynamics from short (nanosecond) time scale MD simulations is fairly consistent with the dynamics of the coarse-grained protein model - the CABS model. The CABS model employs stochastic dynamics (a Monte Carlo method) and a knowledge-based force-field, which is not biased toward the native structure of a simulated protein. Since CABS-based dynamics allows for the simulation of entire folding (or multiple folding events) in a single run, integration of the CABS approach with all-atom MD promises a convenient (and computationally feasible) means for the long-time multiscale molecular modeling of protein systems with atomistic resolution. }
}