title: POPC @ 310K, varying amounts of NaCl. Slipids with ECC-scaled ions
author: Javanainen, Matti
description: Simulations of a POPC bilayer with varying amounts of NaCl. These simulations were performed as a part of the NMRlipids project (http://nmrlipids.blogspot.fi). The goal was to study  the effect of salt on the order parameters of the lipid head  group and the glycerol backbone. The obtained results are  reported in the blog. A POPC bilayer consisting of 200 lipids (100 per leaflet) is  simulated in the presence of NaCl. Concentrations of 130, 300,  500, 750, and 1000 mM are employed. The Slipids model [1–3] is  employed for lipids, tip3p model for water, and the recent ion  parameters by Kohagen et al. [4] for NaCl.  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 named based on the concentration of NaCl and are in GROMACS format. Trajectories (.xtc) are  100 ns long with data saved every 100 ps. Additionally, initial structures (.gro), topology (.top), index (.ndx) and binary run input files for GROMACS v. 4.6–> (.tpr) are provided. The run parameter file (.mdp) is general for all systems. –––––––––––––––––––––––––––––––––––––––––––––––––––––– [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] Accounting for Electronic Polarization Effects in Aqueous Sodium  Chloride via Molecular Dynamics Aided by Neutron Scattering Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth The Journal of Physical Chemistry B Article ASAP DOI: 10.1021/acs.jpcb.5b0522