title: POPC @ 310K, 450 mM of CaCl_2. Charmm36 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 Charmm36  model is employed for lipids, the Charmm compatible variant  of the tip3p model for water, and the recent ion parameters  by Kohagen et al. [2] for CaCl_2. The Charmm36 force field parameters were obtained from CHARMM-GUI [3] at http://www.charmm-gui.org 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 700 ns of simulation. Additionally, the initial  structure (.gro), topology (.top), index file (.ndx),  simulation paremeter file (.mdp), binary run input file  for GROMACS v. 5.0–> (.tpr) and the energy output file  (.edr) are provided.  –––––––––––––––––––––––––––––––––––––––––––––––––––––– [1] Update of the CHARMM All-Atom Additive Force Field  for Lipids: Validation on Six Lipid Types Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites,  Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez,  Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor The Journal of Physical Chemistry B 2010 114 (23), 7830-7843 DOI: 10.1021/jp101759q [2] 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 [3] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM,  and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman,  Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi,  Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III,  Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im Journal of Chemical Theory and Computation 2016 12 (1), 405-413 DOI: 10.1021/acs.jctc.5b00935