LipidMem-BigSMILES (LiMBS): A Standardized Representation Language for Lipid Membrane Systems

Abstract

Molecular dynamics simulations of lipid membranes lack a standardized, machine-readable representation, creating significant barriers to reproducibility, data sharing, and AI-driven analyses. Current membrane descriptions are fragmented across software-specific input files, making it difficult to reconstruct published systems or compare results among studies. Here, we introduce LipidMem-BigSMILES (LiMBS), a line notation not a simulation tool or membrane-building program, for lipid membrane simulations that extend SMILES, BigSMILES, and CG-BigSMILES to membrane systems. LiMBS version 1.0 uses a dual-block architecture that separates a system-level descriptor block from a chemical structure block, enabling the independent specification of membrane geometry, composition, environmental conditions, and molecular identity. The framework supports planar bilayers, vesicles, and bacterial outer membranes in atomistic, coarse-grained, and supercoarse-grained resolutions within a unified syntax. We provide a reference tool that reads, checks, and standardizes LiMBS strings, and we show that its output can be handed off to existing membrane-building software for system construction. LiMBS1.0 is human-readable, machine-readable, tool-independent, and compatible with FAIR data principles, providing a standardized description layer for membrane simulations that supports reproducible reporting, interoperable databases, and AI-enabled membrane biophysics.