Tutorial for Atomistic and Coarse-Grained Simulations of Membrane-Nanoplastic Interactions Using GROMACS

Abstract

Molecular dynamics (MD) simulations are widely used to investigate membrane properties and their interactions with various plastic particles. In this tutorial, we provide guidelines for both atomistic and coarse-grained MD simulations to investigate interactions between a POPC membrane and a polystyrene (PS) nanoplastic. This tutorial is organized into a few exercises focusing on three systems: (i) PS in water, (ii) POPC membrane in water, and (iii) POPC–PS complex in water, each simulated at atomistic and coarse-grained levels. The aim of this tutorial is to familiarize readers with the process of modeling nanoplastic and membrane systems using CHARMM-GUI and performing MD simulations with GROMACS. In addition, we calculate a few biophysical properties, including the radius of gyration of PS, membrane thickness, area per lipid, order parameters, and diffusion coefficient of POPC lipids, using GROMACS analysis tools and tcl scripts. Overall, the workflow presented here provides a practical guide for readers to model, simulate, and analyze their own complex biophysical systems involving membranes and nanoplastics.