(502c) Studying the Importance of Preserving Symmetry in Coarse-Grained Alkanes

In this study we compare different symmetric and asymmetric coarse-grained (CG) mapping operators to understand the importance of preserving symmetry while choosing a CG mapping operator. CG simulations have been widely used to study systems that span large spatiotemporal scales. Selecting a CG mapping operator and obtaining the corresponding potentials are the key steps towards defining a CG model. Both these choices significantly affect how closely a CG simulation reproduces results from the corresponding all-atom (AA) simulation. While there has been considerable progress towards systematically deriving CG potentials, the choice of CG mapping operator is conventionally made using chemical intuition. Recently, there have been efforts towards developing more systematic approaches for defining a CG mapping operator. There is a lack of comprehensive studies on different factors that might influence the efficiency of CG mapping operators. Here we compared different CG mapping operators of alkanes and their isomers to investigate if it is important to preserve the symmetry present in the original alkane molecule while choosing a CG mapping operator. We considered two alkanes, hexane and octane, and three of their isomers. For each isomer, symmetric and asymmetric CG mapping operators were used to perform bottom-up CG simulations. The CG mapping operators were evaluated based on how closely the CG simulation results matched with the structural and dynamic properties obtained from the corresponding all atom simulation. We explored unsupervised cluster analysis as an evaluation metric for CG simulations. This study would contribute towards developing rigorous and systematic strategies, going beyond chemical intuition, to choose effective CG mapping for a molecule.