Paper Citing NAMD - Abstract
Liu, Lin; Gronenborn, Angela M.; Bahar, Ivet
Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:616-625, FEB 2012
Recent studies suggest that protein motions observed in molecular simulations are related to biochemical activities, although the computed time scales do not necessarily match those of the experimentally observed processes. The molecular origin of this conflicting observation is explored here for a test protein, cyanovirin-N (CV-N), through a series of molecular dynamics simulations that span a time range of three orders of magnitude up to 0.4 mu s. Strikingly, increasing the simulation time leads to an approximately uniform amplification of the motional sizes, while maintaining the same conformational mechanics. Residue fluctuations exhibit amplitudes of 12 angstrom in the nanosecond simulations, whereas their average sizes increase by a factor of 45 in the microsecond regime. The mean-square displacements averaged over all residues (y) exhibit a power law dependence of the form y proportional to x0.26 on the simulation time (x). Essential dynamics analysis of the trajectories, on the other hand, demonstrates that CV-N has robust preferences to undergo specific types of motions that already can be detected at short simulation times, provided that multiple runs are performed and carefully analyzed. Proteins 2012. (C) 2011 Wiley Periodicals, Inc.
