DOI: 10.5281/zenodo.15984151
title: Simulations of DPPC:POPC:POPG:CHOL 10:5:3:2 monolayers on air/water interface at varying surface pressure

description: Molecular dynamics simulations of DPPC:POPC:POPG:CHOL 10:5:3:2 monolayers on air/water interface 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 system contains two symmetric monolayers with 128 lipids (64 DPPC, 32 POPC, 19 POPG, and 13 CHOL), potassium ions for charge neutralization, c.a. 30 000 water molecules between the monolayers, and a vacuum slab. Molecular dynamics parameter file (*.mdp) which, except for the surface tension value, is the same for all systems, is included as a separate file (gromppSurf.mdp).

The system was simulated with 5 independent starting configurations, as indicated with the systemX in the archive name.

The files for each system include:



starting system configurations (*-start.gro files)

index files (*.ndx)

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

MD trajectories for the last 70 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 (120-170 ns)

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).

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