Simulations of POPC/POPS membranes with CaCl_2.

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 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 'OPPS'. The starting configurations for the new files were generated by CHARMM-GUI.

The new and corrected files are called "PCPS_CACL_x, where x is the concentration of CaCl_2. 

Final concentrations differ from the initial as ions adsorb to the membrane. Concentration calculated as #ion/#water = [ion]/[water], where [water]=55M.

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 same system with 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  calcium-containing 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. Simulation parameters common for all systems are given in the .mdp file. Simulations were performed with Gromacs 2016.3 [4]

For each CaCl_2 concentration, the trajectory (.xtc), energy file (.edr), run input file (.tpr), index file (.ndx), topology file (.top), and the final structure (gro) are provided. 

[1] Maciejewski et al., J. Phys Chem. B 118, 2014, pp. 4571–4581, DOI: 10.1021/jp5016627 

[2] Kulig et al., Data in Brief 5, 2015, pp. 333–336, DOI: 10.1016/j.dib.2015.09.013

[3] Rog et al., Data in Brief 7, 2016, pp. 1171–1174, DOI: 10.1016/j.dib.2016.03.067

[4] Abraham et al., SoftwareX 1–2, 2015, pp. 19–25, DOI: 10.1016/j.softx.2015.06.001