Curvature elasticity governs size-dependent band-like domain organization in phase-separating nanoscale vesicles

The files provided in this repository are organized into five directories: configurations, mdp, topology, trajectories, and analysis. configurations/ contains the initial and final configurations in GROMACS .gro format. For each trajectory, files labeled *_full.gro contain the complete system including lipids, water, and ions, whereas *_lipid.gro files contain lipid coordinates only. Files labeled *_conf_*.gro correspond to the initial configurations, and *_confout_*.gro correspond to the final configurations after the production simulations. mdp/ contains the GROMACS molecular dynamics parameter files used for the production simulations. PE_grompp.mdp was used for the PE simulations and RV_grompp.mdp for the RV simulations. The production durations were 80 μs and 25 μs, respectively; all other parameters are identical. topology/ contains the GROMACS topology files for the four system groups: PE-A_topol.top, PE-B_topol.top, RV-A_topol.top, and RV-B_topol.top. The Martini parameter files referenced by these topologies (martini_v2.2.itp, martini_v2.0_lipids.itp, and martini_v2.0_ions.itp) are provided in the same directory. trajectories/ contains representative lipid trajectories in GROMACS .xtc format. Only lipid coordinates are included, with frames saved at 1 ns intervals. analysis/ contains the analysis code (Helfrich_free_energy_single_trj.ipynb, Helfrich_free_energy_statistics.ipynb) and its input data. DAT/ stores the per-leaflet lipid coordinates used as notebook inputs. Files named {SYSTEM}_{LEAFLET}_{LIPID}.dat contain the cross-sectional coordinates (r,z) for each lipid type (DIPC, DPPC, or CHOL) in the inner or outer leaflet. A total of 96 files are provided for the 16 systems. Helfrich_free_energy_single_trj.ipynb evaluates, for a single trajectory, the Helfrich bending and line free energies of the observed 3-domain configuration and a geometry-matched 2-domain configuration, as well as their free-energy difference, under the four models. It also reports the critical vesicle size and Ld area fractions at which the free-energy difference is zero. Helfrich_free_energy_statistics.ipynb applies the same analysis to all 16 independent trajectories and reports the ensemble-averaged free-energy differences and stability boundaries (mean ± standard deviation).