Dataset Open Access

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

Javanainen, Matti


JSON-LD (schema.org) Export

{
  "description": "<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 http://www.charmm-gui.org</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>", 
  "license": "http://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "TUT", 
      "@id": "https://orcid.org/0000-0003-4858-364X", 
      "@type": "Person", 
      "name": "Javanainen, Matti"
    }
  ], 
  "url": "https://zenodo.org/record/3237420", 
  "datePublished": "2016-10-09", 
  "@context": "https://schema.org/", 
  "distribution": [
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol0_500ns.cpt", 
      "@type": "DataDownload", 
      "fileFormat": "cpt"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol0_500ns.xtc", 
      "@type": "DataDownload", 
      "fileFormat": "xtc"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol0.edr", 
      "@type": "DataDownload", 
      "fileFormat": "edr"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol0.gro", 
      "@type": "DataDownload", 
      "fileFormat": "gro"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol0.ndx", 
      "@type": "DataDownload", 
      "fileFormat": "ndx"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol0.top", 
      "@type": "DataDownload", 
      "fileFormat": "top"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol0.tpr", 
      "@type": "DataDownload", 
      "fileFormat": "tpr"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol0.xtc", 
      "@type": "DataDownload", 
      "fileFormat": "xtc"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol10_500ns.cpt", 
      "@type": "DataDownload", 
      "fileFormat": "cpt"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol10_500ns.xtc", 
      "@type": "DataDownload", 
      "fileFormat": "xtc"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol10.edr", 
      "@type": "DataDownload", 
      "fileFormat": "edr"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol10.gro", 
      "@type": "DataDownload", 
      "fileFormat": "gro"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol10.ndx", 
      "@type": "DataDownload", 
      "fileFormat": "ndx"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol10.top", 
      "@type": "DataDownload", 
      "fileFormat": "top"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol10.tpr", 
      "@type": "DataDownload", 
      "fileFormat": "tpr"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol10.xtc", 
      "@type": "DataDownload", 
      "fileFormat": "xtc"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol20_500ns.cpt", 
      "@type": "DataDownload", 
      "fileFormat": "cpt"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol20_500ns.xtc", 
      "@type": "DataDownload", 
      "fileFormat": "xtc"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol20.edr", 
      "@type": "DataDownload", 
      "fileFormat": "edr"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol20.gro", 
      "@type": "DataDownload", 
      "fileFormat": "gro"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol20.ndx", 
      "@type": "DataDownload", 
      "fileFormat": "ndx"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol20.top", 
      "@type": "DataDownload", 
      "fileFormat": "top"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol20.tpr", 
      "@type": "DataDownload", 
      "fileFormat": "tpr"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol20.xtc", 
      "@type": "DataDownload", 
      "fileFormat": "xtc"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol30_500ns.cpt", 
      "@type": "DataDownload", 
      "fileFormat": "cpt"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol30_500ns.xtc", 
      "@type": "DataDownload", 
      "fileFormat": "xtc"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol30.edr", 
      "@type": "DataDownload", 
      "fileFormat": "edr"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol30.gro", 
      "@type": "DataDownload", 
      "fileFormat": "gro"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol30.ndx", 
      "@type": "DataDownload", 
      "fileFormat": "ndx"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol30.top", 
      "@type": "DataDownload", 
      "fileFormat": "top"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol30.tpr", 
      "@type": "DataDownload", 
      "fileFormat": "tpr"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol30.xtc", 
      "@type": "DataDownload", 
      "fileFormat": "xtc"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/md.mdp", 
      "@type": "DataDownload", 
      "fileFormat": "mdp"
    }
  ], 
  "identifier": "https://doi.org/10.5281/zenodo.3237420", 
  "@id": "https://doi.org/10.5281/zenodo.3237420", 
  "@type": "Dataset", 
  "name": "POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force field."
}
876
1,870
views
downloads
All versions This version
Views 876753
Downloads 1,8701,677
Data volume 279.4 GB270.9 GB
Unique views 708646
Unique downloads 286220

Share

Cite as