DOI: 10.5281/zenodo.15862877
title: Simulations of DPPC:POPC:POPG:CHOL 10:5:3:2 bilayers with polystyrene chains of 20, 50, and 90 repeat units

description: Molecular dynamics simulations of DPPC:POPC:POPG:CHOL 10:5:3:2 bilayers with adsorbed polystyrene (PS) chains at T = 310 K, p = 1 bar.

CHARMM36 lipid force fields are used for lipids [1,2] and PS [3], OPC model [4] is used for water. Simulations are performed with GROMACS 2022 software [5]. 

Each LSbil system contains a symetric bilayer of 128 or 256 lipids/leaflet (64 or 128 DPPC, 32 or 64 POPC, 19 or 38 POPG, and 13 or 26 CHOL) and one PS chain residing in the hydrophobic core. Bilayers are neutralized with potassium ions, and placed in a box of c.a. 30 000 water molecules. Molecular dynamics parameters, which are the same for all systems, are included as a separate file (grompp310NpT.mdp).

The name of each archive denotes the bilayer size (128 or 256) and the length of PS chain present (PSXX) in the system: 20, 50, or 90 repeat units. Each bilayer/PS system was simulated with 5 independent starting configurations. This is indicated with the systemX appendix in the archive name.

The files for each system include:



starting system configuration (*-start.gro files)

index (*.ndx) and topology (*top) files

full MD trajectories, sampled every 1 ns (*-full.xtc files), with the matching *-full.edr files

*.log files for each full simulation (480-750 ns), which are not concatenated, and are labelled part1, part2, part3, ...

MD trajectories for the last 100 ns of each simulation, sampled every 100 ps (*-final.xtc files), with the matching *.edr files - this simulation data was used to calculate average quantities, such as density profiles, order parameters, etc., discussed in the publication

final system configurations (*-final.gro and *-final.cpt files)


A common directory containing toppar files (*.itp) is included in a separate archive (poly-c36-opc.tar.gz).

This dataset is part of a series of uploads collecting research data used to prepare the publiaction:"Interactions of ultra-fine polystyrene nanoparticles with lung surfactant monolayers and bilayers: A combined molecular dynamics and experimental study"By: Franciszek Włodek, Wojciech Pajerski, Agnieszka Olżyńska, Katarina Vazdar, Petro Khoroshyy, Lukasz Cwiklik, Anna Stachowicz-KuśnierzSubmitted to Journal of Hazardous Materials, July 2025

All records connected with this publication include:



Simulations of clean DPPC:POPC 1:1 monolayers at varying surface pressureDOI: 10.5281/zenodo.15879042

Simulations of DPPC:POPC 1:1 monolayers with polystyrene chains of 20, 50, and 90 repeat units at varying surface pressureDOI: 10.5281/zenodo.15782163

Simulations of clean DPPC:POPC:POPG:CHOL 10:5:3:2 monolayers at varying surface pressureDOI: 10.5281/zenodo.15984151

Simulations of DPPC:POPC:POPG:CHOL 10:5:3:2 monolayers with polystyrene chains of 20, 50, and 90 repeat units at varying surface pressureDOI: 10.5281/zenodo.15847713

Simulations of clean DPPC:POPC:POPG:CHOL 10:5:3:2 bilayers of 128 and 256 lipids/leafletDOI: 10.5281/zenodo.15983030

Simulations of DPPC:POPC:POPG:CHOL 10:5:3:2 bilayers of 128 and 256 lipids/leaflet with polystyrene chains of 20, 50, and 90 repeat unitsDOI: 10.5281/zenodo.15862877

Experimental dataDOI: 10.5281/zenodo.16421262