Abstract
Coarse-grained (CG) models can provide computationally efficient and conceptually simple characterizations of soft matter systems. While generic models probe the underlying physics governing an entire family of free-energy landscapes, bottom-up CG models are systematically constructed from a higher-resolution model to retain a high level of chemical specificity. The removal of degrees of freedom from the system modifies the relationship between the relative time scales of distinct dynamical processes through both a loss of friction and a “smoothing” of the free-energy landscape. While these effects typically result in faster dynamics, decreasing the computational expense of the model, they also obscure the connection to the true dynamics of the system. The lack of consistent dynamics is a serious limitation for CG models, which not only prevents quantitatively accurate predictions of dynamical observables but can also lead to qualitatively incorrect descriptions of the characteristic dynamical processes. With many methods available for optimizing the structural and thermodynamic properties of chemically-specific CG models, recent years have seen a stark increase in investigations addressing the accurate description of dynamical properties generated from CG simulations. In this review, we present an overview of these efforts, ranging from bottom-up parameterizations of generalized Langevin equations to refinements of the CG force field based on a Markov state modeling framework. We aim to make connections between seemingly disparate approaches, while laying out some of the major challenges as well as potential directions for future efforts.
Highlights
Particle-based, low-resolution molecular simulation models, which represent groups of atoms with a single coarse-grained (CG) site, have been instrumental in shaping our perspective of soft matter systems
As early as the 1930s, both Onsager and Kirkwood discussed the concept of the many-body potential of mean force (MB-PMF)—a state-point-dependent free-energy function which acts as the proper CG interaction potential for reproducing all structural and thermodynamic properties of the underlying system at the CG level of resolution [4,5]
Equation (6) simplifies to a form which corresponds to the dissipative particle dynamics (DPD) approach [25]: dP I
Summary
Particle-based, low-resolution molecular simulation models, which represent groups of atoms with a single coarse-grained (CG) site, have been instrumental in shaping our perspective of soft matter systems. Is the direct connection to the true dynamical time scales of the system lost, but the distribution of pathways sampled by a CG model may be qualitatively incorrect To better understand this concept, it is useful to consider the evolution of the system over the free-energy landscape determined by the CG potential and corresponding equations of motion (Figure 1). For chemically-specific CG models, the situation is complicated by incorporating finer details into the model which, if not performed carefully, may lead to a misleading description of the characteristic dynamical processes In this case, researchers have approached the problem by: (i) explicitly correcting the dynamics following the MZ framework; (ii) employing empirical rescaling relations, valid for particular classes of systems, to match specific transport properties; or (iii) refining the CG interaction potential in an attempt to represent the hierarchy of long-time scale processes (i.e., kinetic properties) through the reproduction of the dominant free-energy barriers. In contrast to the original application of MZ to model the evolution of macroscopic observables [9,10,14,15,16,17], e.g., scattering functions [18], we focus here on modeling the time evolution of CG sites that represent groups of atoms
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