Popc @ 310K, 450 Mm Of Cacl_2. Slipids With Ecc-Scaled Ions

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