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Abstract
Two new approaches are presented for obtaining coarse-grained (CG) force fields from atomistic molecular dynamics (MD) trajectories. The first approach is the force-matching (FM) method whereby the force data obtained from an explicit atomistic MD simulation are utilized to determine the CG force fields. The performance of the FM method is demonstrated by applying it to derive a CG model for the dimyristoylphosphatidylcholine (DMPC) lipid bilayer. The second approach is the fluctuation-matching method whereby the fluctuations of specific internal coordinates are extracted from atomistic MD simulations to derive the CG force field. The fluctuation matching method is then applied to analyze the mechanical behavior of actin filaments. Both methods propagate the information obtained at a fine-grained atomistic scale to a CG scale, and hence are termed as multiscale coarse-graining approaches. Such multiscale approaches provide a new route to model complex biomolecular systems.
Acknowledgements
This research was supported by grants from the National Institutes of Health (GM-063796), National Science Foundation (CHE-0218739), and a Faculty Award from the International Business Machines (IBM) Corporation. The authors also thank the National Science Foundation through TeraGrid computational resources provided by the National Center for Supercomputing Applications and the National Institutes of Health (Grant # NCRR 1 S10RR17214-01) on the Arches Metacluster, administered by the University of Utah Center for High Performance Computing.