FATSLIM: Analysis of Lipid Membrane MD Simulations Made Easy

Abstract

Thanks to both the number-crunching power of an average computer, Molecular Dynamics (MD) simulations have been widely used. This increase of computational power leads to inflation of the size and duration of the MD simulations. The analysis of MD trajectories may then become problematic because the generated files may not be handled easily due their size and because extracting/calculating data from atom coordinates stored in the trajectories may not be trivial.In order to overcome these difficulties, the development of FATSLiM (“Fast Analysis Toolbox for Simulations of Lipid Membranes”) began. The goal of this software is to analyze and extract physico-chemical data from MD trajectories of membrane systems. Focused on the lipid bilayer properties, FATSLiM is yet capable of extracting lipid bilayer thickness, area per lipid and lateral diffusion which are three of the most common parameters accessible with experimental techniques.Thanks to its robust internal machinery, FATSLiM is also the only tool that can extract experimental data from MD simulations of non-planar lipid bilayers. FATSLiM is then perfectly suited for the analysis of the effect of a protein (or other molecule) on the properties/morphology of a membrane.Because FATSLiM is also designed to be computationally efficient, the time required for the analysis of a MD trajectory is usually reduced by up to 3 orders of magnitude compared to the really few existing analysis tools. For example, extracting the bilayer thickness from the trajectory of a MD simulation of a lipid membrane made of ∼8000 lipids requires less than 2 seconds per frame.Finally, FATSLiM does not need any pretreatment/manipulation of the MD simulation output files prior analysis since it reads native GROMACS format. One is then able to perform analysis of their MD trajectories as the simulation is progressing.