title: The Theory of Ultra-Coarse-Graining. 2. Numerical Implementation.
abstract: The increasing interest in the modeling of complex macromolecular systems in recent years has spurred the development of numerous coarse-graining (CG) techniques. However, many of the CG models are constructed assuming that all details beneath the resolution of CG degrees of freedom are fast and average out, which sets limits on the resolution of feasible coarse-grainings and on the range of applications of the CG models. Ultra-coarse-graining (UCG) makes it possible to construct models at any desired resolution while accounting for discrete conformational or chemical changes within the CG sites that can modulate the interactions between them. Here, we discuss the UCG methodology and its numerical implementation. We pay particular attention to the numerical mechanism for including state transitions between different conformations within CG sites because this has not been discussed previously. Using a simple example of 1,2-dichloroethane, we demonstrate the ability of the UCG model to reproduce the multiconfigurational behavior of this molecular liquid, even when each molecule is modeled with only one CG site. The methodology can also be applied to other molecular liquids and macromolecular systems with time scale separation between conformational transitions and other intramolecular motions and rotations.
authors.affiliation: Department of Chemistry, The James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago , Chicago, Illinois 60637, United States.
authors.forename: Aram
authors.initials: A
authors.lastname: Davtyan
authors.affiliation: Department of Chemistry, The James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago , Chicago, Illinois 60637, United States.
authors.forename: James F
authors.initials: JF
authors.lastname: Dama
authors.affiliation: Department of Chemistry, The James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago , Chicago, Illinois 60637, United States.
authors.forename: Anton V
authors.initials: AV
authors.lastname: Sinitskiy
authors.affiliation: Department of Chemistry, The James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago , Chicago, Illinois 60637, United States.
authors.forename: Gregory A
authors.initials: GA
authors.lastname: Voth