MLLPA: A Machine Learning-assisted Python module to study phase-specific events in lipid membranes

Machine Learning-Assisted Phase Transition Temperatures from Generalized Replica Exchange Simulations of Dry Martini Lipid Bilayers

Accurate estimation of phase transition temperatures has been a longstanding challenge for molecular simulations. Recently, the generalized Replica Exchange technique for estimating phase transition temperatures has allowed for improved sampling of the phase transition; however, it requires a significant number of simultaneous replicas both inside and outside of the transition region leading to costly computational expense. In this work, the recently developed machine learning-assisted lipid phase analysis technique for learning the phase of individual lipids has been combined with generalized Replica Exchange Molecular Dynamics to reduce the overall computational expense of evaluating transition temperatures. This technique is then applied to eight different Dry Martini lipids to demonstrate its ability to describe transition temperatures as a function of chain length and tail saturation.

LiPyphilic: A Python Toolkit for the Analysis of Lipid Membrane Simulations

Molecular dynamics simulations are now widely used to study emergent phenomena in lipid membranes with complex compositions. Here, we present LiPyphilic-a fast, fully tested, and easy-to-install Python package for analyzing such simulations. Analysis tools in LiPyphilic include the identification of cholesterol flip-flop events, the classification of local lipid environments, and the degree of interleaflet registration. LiPyphilic is both force field- and resolution-agnostic, and by using the powerful atom selection language of MDAnalysis, it can handle membranes with highly complex compositions. LiPyphilic also offers two on-the-fly trajectory transformations to (i) fix membranes split across periodic boundaries and (ii) perform nojump coordinate unwrapping. Our implementation of nojump unwrapping accounts for fluctuations in the box volume under the NPT ensemble-an issue that most current implementations have overlooked. The full documentation of LiPyphilic, including installation instructions and links to interactive online tutorials, is available at https://lipyphilic.readthedocs.io/en/latest.