Backmapping with Mapping and Isomeric Information

Abstract

I present a powerful and flexible backmapping tool named Multiscale Simulation Tool (mstool) that converts a coarse-grained (CG) system into all-atom (AA) resolution and only requires AA to CG mapping and isomeric information (cis/trans/chiral). The backmapping procedure includes two simple steps: a) the AA atoms are randomly placed near the corresponding CG beads according to the provided mapping scheme. b) the energy minimization is performed with two modifications in the forcefield. First, the nonbonded interactions are replaced with a cosine function to ensure numerical stability. Second, additional dihedrals are imposed to maintain the molecule's isomeric properties. To test the tool's simplicity and robustness, I have demonstrated a backmapping of the four-bead CG lipid model into the corresponding AA resolution (resolution increased by a factor of 34) without using an intermediate resolution. The tool is freely available at github.com/ksy141/mstool.