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

description: Molecular dynamics simulations of DPPC:POPC:POPG:CHOL 10:5:3:2 monolayers on air/water interface with adsorbed polystyrene (PS) chains, at varying surface tension, T = 310 K, pz = 1 bar. The applied surface tension corresponds to surface pressure of: 2.0, 12.0, 22.0, 32.0, and 39.5 mN/m.

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 LSmono system contains two symmetric monolayers with 128 lipids (64 DPPC, 32 POPC, 19 POPG, and 13 CHOL) and one PS chain, c.a. 30 000 water molecules between the monolayers, potassium ions for charge neutralization, and a vacuum slab. Molecular dynamics parameter files (*.mdp), which, except for the surface tension value, are the same for all systems, are included as separate files. gromppSurf-1.mdp file corresponds to initial simulation stages (c.a. 20 ns), when PS adsorptions takes place. A flat-bottom potential is added to avoid escape of PS from the monolayer. gromppSurf-2.mdp file corresponds to production simulations, with external potentials removed. 

The name of each archive denotes the length of PS achain present (PSXX) in the system: 20, 50, or 90 repeat units. Each monolayer/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 files (*.ndx)

MD trajectories for the last 100 ns of each simulation, sampled every 100 ps (*.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

*.log files for each full simulation (285-370 ns), which are not concatenated, and are labelled part1, part2, part3, ...

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


The files are labelled with the value of surface pressure imposed on the system in each simulation.

A common topology file (*.top) is given in the main directory.

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

Full trajectories, due to large size and number of files, are not included, but are available upon request at stachowa@chemia.uj.edu.pl. 

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