Simulations of POPC/POPS membranes with CaCl_2.

<p>Simulations of POPC/POPS (5:1, 144 lipids in total) membranes with 0, 100, 300, 1000, and 3000 mM of CaCl_2. Additionally, the systems contain 40 waters per lipid, and potassium&nbsp;counter ions for the anionic PS. This is an update to a previous upload in which the PS tails were reversed, so it was actually &#39;OPPS&#39;. The starting configurations for the new files were generated by CHARMM-GUI.</p> <p>The new and corrected files are called &quot;PCPS_CACL_x, where x is the concentration of CaCl_2.&nbsp;</p> <p>Final concentrations differ from the initial as ions adsorb&nbsp;to the membrane. Concentration calculated as #ion/#water = [ion]/[water], where [water]=55M.</p> <p>The lipid model by Maciejewski and Rog [1,2,3] was used. Topologies (.itp) were obtained from [3] and the OPPS chains were reversed (the fixed itp is included in the upload of the simulations of the&nbsp;same system with&nbsp;KCl: https://doi.org/10.5281/zenodo.1404040) to create POPS. TIP3P water was used, and the ions were modelled using default OPLS ion parameters. All &nbsp;calcium-containing&nbsp;simulations were 600 ns long, and the last 300 ns are included in the uploaded trajectories. The calcium-free simulation was 400 ns long and uploaded in its entirety.&nbsp;Simulation parameters common for all systems are given in the .mdp file. Simulations were performed with Gromacs 2016.3 [4]</p> <p>For each CaCl_2 concentration, the trajectory (.xtc), energy file (.edr),&nbsp;run input file (.tpr), index file (.ndx), topology file (.top), and&nbsp;the&nbsp;final structure (gro) are provided.&nbsp;</p> <p>[1] Maciejewski et al., J. Phys Chem. B 118, 2014, pp. 4571&ndash;4581, DOI:&nbsp;10.1021/jp5016627&nbsp;</p> <p>[2] Kulig et al., Data in Brief&nbsp;5, 2015, pp. 333&ndash;336,&nbsp;DOI:&nbsp;10.1016/j.dib.2015.09.013</p> <p>[3] Rog et al., Data in Brief&nbsp;7,&nbsp;2016, pp. 1171&ndash;1174,&nbsp;DOI: 10.1016/j.dib.2016.03.067</p> <p>[4] Abraham et al., SoftwareX&nbsp;1&ndash;2, 2015, pp. 19&ndash;25, DOI:&nbsp;10.1016/j.softx.2015.06.001</p>