@article {260, 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}, year = {2013}, month = {12/2012}, pages = {119 - 125}, 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.}, keywords = {molecular dynamics, near-native dynamics, protein dynamics, protein flexibility, simulation}, isbn = {1549-9618}, doi = {10.1021/ct300854w}, url = {http://dx.doi.org/10.1021/ct300854w}, author = {Michal Jamroz and Modesto Orozco and Andrzej Koli{\'n}ski and Sebastian Kmiecik} }