Dataset Open Access

POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force field.

Javanainen, Matti

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  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.3237420", 
  "title": "POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force field.", 
  "issued": {
    "date-parts": [
  "abstract": "<p>A POPC bilayer consisting of 200 lipids (100 per leaflet)&nbsp;is simulated in the presence of 0% (0 molecules), 10 %&nbsp;(22 molecules), 20 % (50 molecules), or 30 % (86 molecules)&nbsp;of cholesterol.&nbsp;The Charmm36&nbsp;model [1] is employed for lipids and the Charmm-compatible variant&nbsp;of the tip3p model for water.</p>\n\n<p>The Charmm36 force field parameters were obtained from CHARMM-GUI [2] at</p>\n\n<p>*** IMPORTANT&nbsp;***</p>\n\n<p>This is a correction to an earlier dataset simulated with some missing dihedrals, see:&nbsp;DOI: 10.5281/zenodo.61649</p>\n\n<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>\n\n<p>The files are in GROMACS format. Trajectory (.xtc) is&nbsp;100 ns long with data saved every 100 ps. Additionally, the initial&nbsp;structure (.gro), topology (.top), index file (.ndx), simulation paremeter file (.mdp), binary run input file&nbsp;for GROMACS v. 5.0&ndash;&gt; (.tpr) and the energy output file&nbsp;(.edr) are provided.&nbsp;</p>\n\n<p>UPDATE: Longer 500 ns&nbsp;trajectories are updated together with the checkpoint files.</p>\n\n<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>\n\n<p>[1] Update of the CHARMM All-Atom Additive Force Field&nbsp;for Lipids:&nbsp;Validation on Six Lipid Types</p>\n\n<p>Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, &nbsp;Joseph W. O&rsquo;Connor,&nbsp;Douglas J. Tobias, Carlos Mondragon-Ramirez,&nbsp;Igor Vorobyov, Alexander D.&nbsp;MacKerell, Jr., and Richard W. Pastor</p>\n\n<p>The Journal of Physical Chemistry B 2010 114 (23), 7830-7843</p>\n\n<p>DOI: 10.1021/jp101759q</p>\n\n<p>&nbsp;</p>\n\n<p>[2] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM,&nbsp;and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field</p>\n\n<p>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,&nbsp;Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III,&nbsp;Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im</p>\n\n<p>Journal of Chemical Theory and Computation 2016 12 (1), 405-413</p>\n\n<p>DOI: 10.1021/acs.jctc.5b00935</p>", 
  "author": [
      "family": "Javanainen, Matti"
  "type": "dataset", 
  "id": "3237420"
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