Year: 2018
Type: article
Abstract: Coarse-grained (CG) molecular dynamics (MD) can simulate systems inaccessible to fine-grained (FG) MD simulations. A CG simulation decreases the degrees of freedom by mapping atoms from an FG representation into agglomerate CG particles. The FG to CG mapping is not unique. Research into systematic selection of these mappings is challenging due to their combinatorial growth with respect to the number of atoms in a molecule. Here we present a method of reducing the total count of mappings by imposing molecular topology and symmetry constraints. The count reduction is illustrated by considering all mappings for nearly 50 000 molecules. The resulting number of mapping operators is still large, so we introduce a novel hierarchical graphical approach which encodes multiple CG mapping operators. The encoding method is demonstrated for methanol and a 14-mer peptide. With the test cases, we show how the encoding can be used for automated selection of reasonable CG mapping operators.
Source: The Journal of Chemical Physics
DOI: 10.1063/1.5040114
Authors: Maghesree Chakraborty, Chenliang Xu, Andrew D. White
Institution: University of Rochester
Language: English
Subfield: Physical and Theoretical Chemistry
Field: Chemistry
Domain: Physical Sciences
Open Access status: green
Funder: National Science Foundation
OpenAlex ID: W2797170044