POPC @ 310K, 450 mM of CaCl_2. Charmm36 with ECC-scaled ions

<p>Simulations of a POPC bilayer with 450 mM of CaCl_2.&nbsp;<br> The goal was to study the effect of salt on the order&nbsp;<br> parameters of the lipid head group and the glycerol&nbsp;<br> backbone for the NMRlipids project, see&nbsp;<br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet)&nbsp;<br> is simulated in the presence of 450 mM CaCl_2. The Charmm36&nbsp;<br> model is employed for lipids, the Charmm compatible variant&nbsp;<br> of the tip3p model for water, and the recent ion parameters&nbsp;<br> by Kohagen et al. [2] for CaCl_2.</p> <p>The Charmm36 force field parameters were obtained from<br> CHARMM-GUI [3] at http://www.charmm-gui.org</p> <p>The ion parameters are available at<br> https://bitbucket.org/hseara/ions/</p> <p>&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;</p> <p>The files are in GROMACS format. Trajectory (.xtc) is&nbsp;<br> 100 ns long with data saved every 100 ps. These data<br> were collected once the adsorption and desorption of&nbsp;<br> CaCl_2 to the surface has reached equilibrium, namely<br> after 700 ns of simulation. Additionally, the initial&nbsp;<br> structure (.gro), topology (.top), index file (.ndx),&nbsp;<br> simulation paremeter file (.mdp), binary run input file&nbsp;<br> for GROMACS v. 5.0&ndash;&gt; (.tpr) and the energy output file&nbsp;<br> (.edr) are provided.&nbsp;</p> <p>&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;&ndash;</p> <p>[1] Update of the CHARMM All-Atom Additive Force Field&nbsp;<br> for Lipids: Validation on Six Lipid Types<br> Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites,&nbsp;<br> Joseph W. O&rsquo;Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez,&nbsp;<br> Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor<br> The Journal of Physical Chemistry B 2010 114 (23), 7830-7843<br> DOI: 10.1021/jp101759q</p> <p>[2] 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</p> <p>[3] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM,&nbsp;<br> and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field<br> Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman,&nbsp;<br> Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi,&nbsp;<br> Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III,&nbsp;<br> Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im<br> Journal of Chemical Theory and Computation 2016 12 (1), 405-413<br> DOI: 10.1021/acs.jctc.5b00935</p>