DIM_Phase_transition_CG

This work is based on the following repository : https://doi.org/10.5281/zenodo.15173051This repository contains all the data produced regarding phase transition of 4-membrane systems containing different concentrations of DIM lipid, at temperatures ranging from 280 to 350K. The folders contain the resulting xtc trajectories, gro files, and tpr files for reproduction of the calculations. Below, a short description of the methodology : All simulations were performed with GROMACS version 2020.2. We conducted CG simulations of stacked lipid membranes in close proximity using the MARTINI3 force field and home made parameters for the DIM molecule. We built a simulation system consisting of 4 stacked membranes. Each individual membrane contained 154 POPC molecules, 470 DOPE molecules (DOPE/POPC molar ratio 3.05:1) and either 6, 12 or 18 molecules PDIM (PGL/lipid molar ratio 1%, 2%, 3%). The membranes were solvated with Martini 3 CG water (W) particles, with 3.33 W particles per lipid molecule, corresponding to about 13 atomistic water molecules per lipid. To preserve the lamellar membrane phase, the systems were equilibrated at 280 K, using the v-rescale thermostat with a time constant tT = 1.0 ps, and the Berendsen barostat with semi-isotropic pressure coupling, a reference pressure of 1.0 bar, a time constant tp = 5 ps, and a compressibility of 3 × 10-4 bar-1. Then 8 different simulations were launched, with temperatures ranging from 280 K to 350 K in 10 K increments. We executed the production runs in triplicate at each temperature, using a time step of 20 fs, for a total duration of 3 µs. The temperature was controlled using the Berendsen thermostat with a time constant tT = 1.0 ps, while the pressure was set using the Berendsen barostat with fully anisotropic pressure coupling, at a reference pressure of 1.0 bar, a time constant tp = 0.5 ps, and a compressibility of 1.0 × 10-5 bar-1. Constraints were imposed using the LINCS algorithm.The DIM force field parameters, the Python and TCl files necessary to the reproduction of figures are available in the parent repository.