Trajectories of an Air–Water Slab Using the MB-pol Model

Description of the Data and File Structure We provide simulation trajectories of the air–water slab in the following compressed archives Data_1-5.tar.xz Data_6-10.tar.xz Data_11-15.tar.xz Data_16-20.tar.xz . Each archive contains multiple independent trajectories (1-20) stored in separate directories. Data Format All trajectory files are stored in NumPy ".npy" format and can be loaded using import numpy as np Rs = np.load("Rs_curta.npy") . Each array has shape (n_times, n_atoms, 3) where n_times is the number of saved time frames, n_atoms is the number of atoms, and the last dimension corresponds to the Cartesian coordinates (x, y, z) and coordinates are given in angstrom. Molecular Structure Atoms are ordered as O H H O H H ... Each O H H triplet corresponds to a single water molecule. Time Resolution The time between saved frames is 3.2 fs while the simulation time step is 0.2 fs. Trajectories Trajectories 1–20 are included as .npy data files in the archives listed above. All input files required to reproduce all trajectories (1–100) are provided in run_files.zip . This archive contains a script run.sh which can be used to start simulations for example the command bash run.sh 1 starts the simulation from the initial frame 1. Software Requirements Simulations were performed using MB-pol via the Paesani Lab implementation of MBX and LAMMPS and NumPy Python for data handling Installation instructions for MBX are available at https://github.com/paesanilab/MBX.git . Summary of Contents Data_1-5.tar.xz Data_6-10.tar.xz Data_11-15.tar.xz Data_16-20.tar.xz . contains npy files with atomic coordinates of air–water interface trajectories. run_files.zip contains input files and scripts to reproduce simulations and run.sh is a script to launch individual trajectories