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

description: Molecular dynamics simulations of DPPC:POPC 1:1 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: 4.0, 14.0, 22.0, 31.5, and 37.0 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 system contains two symmetric monolayers with 128 lipids and one PS chain, c.a. 30 000 water molecules between the monolayers 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 (280 ns), with external potentials removed. 

The name of each archive denotes the length of PS chain 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 (c.a. 300 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