title: POPC @ 310K, 450 mM of CaCl_2. Slipids with ECC-scaled ions
author: Javanainen, Matti
description: Simulations of a POPC bilayer with 450 mM of CaCl_2.  The goal was to study the effect of salt on the order  parameters of the lipid head group and the glycerol  backbone for the NMRlipids project, see  http://nmrlipids.blogspot.fi for more information. A POPC bilayer consisting of 200 lipids (100 per leaflet)  is simulated in the presence of 450 mM CaCl_2. The Slipids  model [1–3] is employed for lipids, tip3p model for water,  and the recent ion parameters by Kohagen et al. [4] for  CaCl_2. The Slipids force field parameters were downloaded from http://mmkluster.fos.su.se/slipids/ The ion parameters are available at https://bitbucket.org/hseara/ions/ –––––––––––––––––––––––––––––––––––––––––––––––––––––– The files are in GROMACS format. Trajectory (.xtc) is  100 ns long with data saved every 100 ps. These data were collected once the adsorption and desorption of  CaCl_2 to the surface has reached equilibrium, namely after 500 ns of simulation. Additionally, the initial  structure (.gro), topology (.top), index file (.ndx),  simulation paremeter file (.mdp), binary run input file  for GROMACS v. 4.6–> (.tpr) and the energy output file  (.edr) are provided.  –––––––––––––––––––––––––––––––––––––––––––––––––––––– [1] Derivation and Systematic Validation of a Refined  All-Atom Force Field for Phosphatidylcholine Lipids Joakim P. M. Jämbeck and Alexander P. Lyubartsev The Journal of Physical Chemistry B 2012 116 (10), 3164-3179 DOI: 10.1021/jp212503e [2] An Extension and Further Validation of an All-Atomistic  Force Field for Biological Membranes Joakim P. M. Jämbeck and Alexander P. Lyubartsev Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948 DOI: 10.1021/ct300342n [3] Another Piece of the Membrane Puzzle: Extending Slipids Further Joakim P. M. Jämbeck and Alexander P. Lyubartsev Journal of Chemical Theory and Computation 2013 9 (1), 774-784 DOI: 10.1021/ct300777p [4] Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth The Journal of Physical Chemistry B 2014 118 (28), 7902-7909 DOI: 10.1021/jp5005693