Large Dppc Monolayer Simulations With Charmm36+Opc @ 298 K (Part 2/2)

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. This file, together with the topology (.top) and index files (common for all systems) are available in Part 1 of this upload (see below). 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 https://doi.org/10.5281/zenodo.345321 Matti Javanainen, Antti Lamberg, Lukasz Cwiklik, Ilpo Vattulainen, and O. H. Samuli Ollila. <em>Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers</em>, Langmuir <strong>2018</strong> 34 (7), 2565-2572, DOI: 10.1021/acs.langmuir.7b02855 [1] DOI: 10.1021/jp101759q<br> [2] DOI: 10.1021/jz501780a<br> [3] DOI: 10.1016/j.softx.2015.06.001