Backmapping with Mapping and Isomeric Information

Abstract

ABSTRACTI 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/dihedral/chiral). The backmapping procedure includes two simple steps: a) AA atoms are randomly placed near the corresponding CG beads according to the provided mapping scheme. b) Energy minimization is performed with two modifications in the AA force field (FF). First, nonbonded interactions are replaced with cosine functions to ensure numerical stability. Second, additional torsions are imposed to maintain molecules’ isomeric properties. To test the simplicity and robustness of the tool, I backmapped multiple membrane and protein CG structures into AA resolution, including a four-bead CG lipid model (resolution increased by a factor of 34) without using intermediate resolution. The tool is freely available atgithub.com/ksy141/mstool.TABLE OF CONTENTS (TOC)