Large DPPC monolayer simulations with Charmm36+OPC @ 310 K (Part 1/2)

<p>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.&nbsp;</p> <p>The number in the filename corresponds to the area per lipid in &Aring;ngstr&ouml;ms. The starting structures were generated by setting up a POPC monolayer system with an area per lipid of 50&nbsp;&Aring;^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&nbsp;&Aring;^2 were generated by compressing the DPPC monolayer system with PLUMED.</p> <p>All trajectories, 100&ndash;200 ns long (until convergence of surface tension), are simulated with Gromacs 5.0.x [3] using the default Charmm36 monolayer simulations&nbsp;parameters given in the mdp file. Topology (.top) and index files are also common for all simulations.&nbsp;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/ .</p> <p>Part 2 of this upload is available at&nbsp;https://doi.org/10.5281/zenodo.838641</p> <p>Matti Javanainen, Antti Lamberg, Lukasz Cwiklik, Ilpo Vattulainen, and O. H. Samuli Ollila.&nbsp;<em>Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers</em>,&nbsp;Langmuir&nbsp;<strong>2018</strong>&nbsp;34&nbsp;(7), 2565-2572,&nbsp;DOI: 10.1021/acs.langmuir.7b02855</p> <p>[1] DOI: 10.1021/jp101759q<br> [2] DOI: 10.1021/jz501780a<br> [3] DOI: 10.1016/j.softx.2015.06.001</p>