title: POPC @ 310K, 130 mM of NaCl. Slipids with ions by Smith & Dang
author: Javanainen, Matti
description: Simulations of a POPC bilayer with 130 mM of NaCl.  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  NMRlipids blog at http://nmrlipids.blogspot.fi A POPC bilayer consisting of 200 lipids (100 per leaflet)  is simulated in the presence of 130 mM NaCl. The Slipids  model [1–3] is employed for lipids, tip3p model for water,  and the ion parameters by Smith and Dang [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 in GROMACS format. Trajectory (.xtc) is  100 ns long with data saved every 100 ps. 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] Computer simulations of NaCl association in polarizable water David E. Smith and Liem X. Dang  The Journal of Chemical Physics 1994 100, 3757-3766 DOI: 10.1063/1.466363