Supplementary material for "Collective adsorption of pheromones at the water-air interface"

This deposit contains the files resulting from the molecular dynamics simulations of bombykol molecules at the water-air interface using LAMMPS, as studied in the following paper that has been accepted for publication in the Journal of the Royal Society Interface. L. Jami, T. Zemb, J. Casas, and J.-F. Dufrêche. Collective adsorption of pheromones at the water-air interface. https://doi.org/10.48550/arXiv.2512.04340 # thermo_logs.zipCompressed directory containning the logs of LAMMPS of the different simulated systems, providing the thermodynamic data (temperature, energy, surface tension) over time. The compress files are named as 'tens_bombX_woWall_Y' with X the number of bombykol molecule per interface and Y the ID of the simulation job. # xyz_analysis.npy - numpy file to open with the following code in python:import numpy as nprec = np.load('path/xyz_analysis.npy.npy',allow_pickle=True).item()if 'rec' in rec['list_data']: print('rec in list_data (!)')for inc in rec['list_data']: locals()[inc]=rec[inc]del(rec) - this loads the data from atom trajectory analysis. The important variables that are loaded are: - The list of molecular simulation IDs: syst_nums3 - The list of the number of bombykol per interface in each simulation: syst_bomb_nums3 - The single particule statistics Z position: hist_posZ[job][atom][interface][hist_edges] - two particules statistics (r distance): hist_g[job][atom][hist_edges] - the keys of these dictionnaries are: - job IDs given by the syst_nums3 list - atom: 'Ow', 'OH', 'C8', 'C16', 'COM' - interface: 0 (up) or 1 (down) - hist_edges: 0 (hist) or 1 (edges) # topo_file.zip Compressed directory containing the topological data file for each simulated systems. These are input file for LAMMPS also used in the analysis of the results to keep track of the bounds between atoms. Additionaly, raw molecular simuation (.xyz) data can be provided on the demand by the authors.