Title: Large POPC monolayer simulations with Charmm36+OPC @ 298 K (Part 1/2)

Type Dataset Javanainen, Matti (2017): Large POPC monolayer simulations with Charmm36+OPC @ 298 K (Part 1/2). Zenodo. Dataset. https://zenodo.org/record/322830

Author: Javanainen, Matti (TUT) ;

Links

• Item record in Zenodo
• Digital object URL

Summary

POPC monolayers simulated at a varying area per lipid in the NVT ensemble. The Charmm36 lipid model [1] is employed together with the 4-point OPC water model [2]. Each system contains two monolayers with 256 lipids each. These monolayers are separated by a water slab, and surrounded by vacuum. 

The number in the filename corresponds to the area per lipid in Ångströms. The starting structures were generated by setting up a system with an area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was expanded using PLUMED. 

All trajectories, 100 ns long, are simulated with Gromacs 5.0.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. Topology (.top) and index files are also common for all simulations. The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ .

Part 2 of this upload is available at: https://doi.org/10.5281/zenodo.838633

Matti Javanainen, Antti Lamberg, Lukasz Cwiklik, Ilpo Vattulainen, and O. H. Samuli Ollila. Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers, Langmuir 2018 34 (7), 2565-2572, DOI: 10.1021/acs.langmuir.7b02855

[1] DOI: 10.1021/jp101759q [2] DOI: 10.1021/jz501780a [3] DOI: 10.1016/j.softx.2015.06.001

More information

• DOI: 10.5281/zenodo.322830

Dates

• Publication date: 2017
• Issued: February 27, 2017

Rights

• https://creativecommons.org/licenses/by/4.0/legalcode Creative Commons Attribution 4.0 International
• info:eu-repo/semantics/openAccess Open Access

Format

electronic resource

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