DPPC/POPC/POPG/CHL1 Monolayer Simulations With Charmm36+OPC (Part 1/4)
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2020-10-31, 2020-10-31
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DPPC/POPC/POPG/CHL1 (60/20/10/10 mol-%) monolayers simulated at varying area per lipid and temperature in the NVT ensemble. The Charmm36 lipid model [1] is used together with the 4-point OPC water model [2]. Each system consist of two monolayers with 169 lipids each. The monolayers are separated by a water slab, and surrounded by vacuum.
The numbering in the filenames corresponds to the area per lipid in Ångströms * 10, temperature, possible independent repetitions (2 and 3). The starting structures were generated with CHARMM-GUI with an initial area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was either compressed or expanded using PLUMED.
All trajectories are simulated for 1000 ns with Gromacs 5.1.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 1 of this upload is available at: DOI:10.5281/zenodo.3898344
Part 2 of this upload is available at: DOI:10.5281/zenodo.3899875
Part 3 of this upload is available at: DOI:10.5281/zenodo.3899535
Part 4 of this upload is available at: DOI:10.5281/zenodo.4034250
Juho Liekkinen, Berta de Santos Moreno, Riku O. Paananen, Ilpo Vattulainen, Luca Monticelli, Jorge Bernardino de la Serna, and Matti Javanainen. Understanding the Functional Properties of Lipid Heterogeneity in Pulmonary Surfactant Monolayers at the Atomistic Level. Frontiers in Cell and Developmental Biology - Cellular Biochemistry (2020)
doi: 10.3389/fcell.2020.581016
[1] DOI: 10.1021/jp101759q
[2] DOI: 10.1021/jz501780a
[3] DOI: 10.1016/j.softx.2015.06.001