Simulations of POPC/POPS membranes with KCl

Simulations of POPC/POPS (5:1, 144 lipids in total) membranes with 500, 1000, 2000, and 3000 mM of KCl. This is an update to a previous upload in which the PS tails were reversed, so it was actually 'OPPS'. Moreover, at 4000 mM of KCl the ions formed a crystal, so these data are omitted. The starting configurations were generated by CHARMM-GUI.

The files of the old submission are called  "PCPS-KClx" with 'x' indicating the concentration of KCl, whereas the new and corrected files are called "PCPS_KCL_x. 

Simulations of the same membrane in the presence of only counterions as well as in the presence of different amounts of CaCl_2 are available in DOI:10.5281/zenodo.897467

The systems contain 40 waters per lipid, and additional potassium counter ions for the anionic PS. Final concentrations differ from the initial as ions adsorb to the membrane. Concentration calculated as #ion/#water = [ion]/[water], where [water]=55.5 M.

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) to create POPS. TIP3P water was used, and the ions were modelled using default OPLS ion parameters. All simulations are 300 ns long and the uploaded trajectories contain the last 200 ns. Simulation parameters common for all systems are given in the md.mdp file. Simulations were performed with Gromacs 2016.3 [4].

For each KCl concentration, the trajectory (.xtc), energy file (.edr), checkpoint file (.cpt), 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