Is preservation of symmetry necessary for coarse-graining?

Abstract

<p>This work investigates if preserving the symmetry of the underlying molecular graph of a given molecule when choosing a coarse-grained (CG) mapping significantly affects the CG model accuracy.</p>

Graph neural network based coarse-grained mapping prediction

“…Thus far, the model has been judged against human-annotated mappings and not in molecular dynamics simulation. To assess the predicted mappings, we draw upon the simulation results from recent work by Chakraborty et al 11 where force matching was used for coarse-graining. We have compared the performance of the CG mappings predicted by DSGPM for 6 alkane molecules with multiple CG bead numbers, giving 22 different simulation results.…”

“…We have compared the performance of the CG mappings predicted by DSGPM for 6 alkane molecules with multiple CG bead numbers, giving 22 different simulation results. The individual mappings of the 6 alkane molecules (nhexane, isohexane, 2,3-dimethylbutane, n-octane, 3-ethylhexane, and 4-methylheptane) that were considered in Chakraborty et al 11 and those predicted by DSGPM are shown in Fig. S2.…”

“…4 COM-RDF square errors as previously reported for CG mappings of 6 alkane molecules. 11 The mappings for each molecule have been categorized into colored blocks corresponding to the number of CG beads. For each block, the mappings are arranged in the order of increasing AMI values, as indicated below the CG mapping labels.…”

“…This is supported by a recent study of 26 CG mappings for 7 alkane molecules that found little correlation between mapping resolution and CG model performance. 11 There is not only a lack of methods to compute mapping operators, there is no agreed upon goal in choosing mapping operators.…”

Chemically specific coarse‐graining of polymers: Methods and prospects

“…To capture the effects of hydrogen bonding in cellulose nanostructures, this CG representation uses a combination of backbone, linker, satellite, and hydrogen bonding beads for each glucopyranose monomer. Images adapted with permission from Reference 155, copyright 2020, American Chemical Society found that topological symmetry, which refers to the symmetry of the underlying molecular graph, was relatively unimportant in reproducing both structural and dynamic properties by comparison to asymmetric models with the same CG resolution, also irrespective of the method of parameterization 136 ; similar observations can be drawn from other work by Khot et al, 137 although it did not explicitly attempt to control for or elucidate the role of symmetry. Thus, while it seems that more nuanced mapping operators (compared to COM mapping) can be sometimes beneficial, it is not yet evident when to pursue such strategies for polymer modeling.…”