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

DPPC 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 POPC monolayer system with an area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was expanded using PLUMED. Next, POPC was replaced by DPPC, and the systems were energy minimized. Systems with area smaller than 51 Å^2 were generated by compressing the DPPC monolayer system with PLUMED.

All trajectories, 100–200 ns long (until convergence of surface tension), 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.838635

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