Wavelet Analysis for Molecular Dynamics
Abstract
We present a multiresolution diffusion-wavelet approach to operator compression, which does not require explicit preparation of atomistic-to-coarse-grained mappings. Our method takes as input the topology and sparsity of the bonding structure of a molecular system, and returns a hierarchical set of system-specific coarse-grained (CG) variables. The hierarchical compression provides a clear framework for modeling at many model scales (levels), beyond the common 2-level CG representation. Our results show that the hierarchy separates localized modes from larger-scale motions, e.g., long-range concerted backbone vibrational modes. Our approach correctly captures small-scale chemical features as well as large-scale features of the backbone. In particular, the new method's finest-scale modes are comparable to united atom models and other chemically defined CG models. Modes at coarser levels describe increasingly large connected portions of the target polymers. For polyethylene and polystyrene, spatial coordinates and their associated forces were compressed by up to 2 orders of magnitude. The compression in forces is of particular interest as this allows larger time steps as well as reducing the number of degrees of freedom.
Document Details
- Document Type
- Technical Report
- Publication Date
- Jun 01, 2015
- Accession Number
- ADA619816
Entities
People
- Ahmed E. Ismail
- Berend C. Rinderspacher
- Jaydeep P. Bardhan
Organizations
- United States Army Research Laboratory