Fig. 1

Interplay between different encoding levels of molecular structures for a preparation step of a molecular simulation task (with examples of this work, compare Figs. 2, 4 and 5). a Structural formula of a DMPC phospholipid. b SPICES line notation of the particle-based topological DMPC structure with its corresponding structure diagram layout/particle graph and illustration of the particle bonds. c Conversion of the topological particle structure to a compressed 3D tube geometry plus spatial mapping into an oriented bilayer compartment of the simulation box