title: Source molecular simulation data for calculating energy and friction profiles and permeability coefficients through model lipid membranes
author: Melcr, Josef
description: Energy files from GROMACS molecular dynamics simulations with enhanced free energy sampling contain time-dependent evolution of the free energy profiles and friction profiles (and other energies and simulation properties) that were used for calculating permeability coefficients in the publication https://www.biorxiv.org/content/10.1101/2021.07.16.452599v1 Simulation system contains a lipid POPC or DPPC bilayer with a varying amount of cholesterol (specified as mol% in the file name). Hydrophobic level of the permeating particle is specified as "level-I", "level-II" etc. When unspecified in the file name, the particle is hydrophobic level "III". Lipids D-C14-PC denote PC lipids with both tails monounsaturated of length 14 carbon atoms. DOPC is equivalent to D-C18-PC. (Detailed description in the publication) Adaptive Weighted Histogram (AWH) method was used to sample the free energy profile of translocating small molecule through the lipid bilayer. GROMACS tool `gmx awh` reads the files and provides the described profiles. Files were generated by GROMACS `mdrun` simulation engine version 2019.3.   Coarse-grained MARTINI 3.0 model was used for modeling the biomolecular interactions. Scripts to perform the simulations and the files with initial configurations and simulation settings are stored in a public GitHub repository depozited on Zenodo.org: https://doi.org/10.5281/zenodo.5082249.   Abraham, M. J. et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25 (2015). Lindahl, V., Lidmar, J. & Hess, B. Accelerated weight histogram method for exploring free energy landscapes. J. Chem. Phys. 141, 044110 (2014). Souza, P. C. T. et al. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nat. Methods 18, 382–388 (2021). Melcr, J. Git repository with analysis scripts for MD simulations of permeability through lipid membranes. (2021) doi:https://doi.org/10.5281/zenodo.5082249.