Dataset Open Access

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

Javanainen, Matti


JSON Export

{
  "files": [
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol0_500ns.cpt"
      }, 
      "checksum": "md5:46e5c9f081c9a0f080fff578e9be64f6", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol0_500ns.cpt", 
      "type": "cpt", 
      "size": 1293272
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol0_500ns.xtc"
      }, 
      "checksum": "md5:7b5c997e5ae0ac22c160671e11e8bb25", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol0_500ns.xtc", 
      "type": "xtc", 
      "size": 995117612
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol0.edr"
      }, 
      "checksum": "md5:e195c66512fd220730585a69d414286d", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol0.edr", 
      "type": "edr", 
      "size": 31201356
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol0.gro"
      }, 
      "checksum": "md5:de691db00ccc75eb4cc2659997dc98c6", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol0.gro", 
      "type": "gro", 
      "size": 3712252
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol0.ndx"
      }, 
      "checksum": "md5:a054230c11ff4c0d38a20385381d1014", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol0.ndx", 
      "type": "ndx", 
      "size": 1265618
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol0.top"
      }, 
      "checksum": "md5:92016a55a5c8f2e8eed000b4bc9a0813", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol0.top", 
      "type": "top", 
      "size": 146
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol0.tpr"
      }, 
      "checksum": "md5:5cbd58ce79e96e1cfcb42215a3af234b", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol0.tpr", 
      "type": "tpr", 
      "size": 1765892
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol0.xtc"
      }, 
      "checksum": "md5:954ab17e0385c6bef4f5b60d8e220e97", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol0.xtc", 
      "type": "xtc", 
      "size": 199181816
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol10_500ns.cpt"
      }, 
      "checksum": "md5:66ccc4d1290e7a3534df9794c10dcb01", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol10_500ns.cpt", 
      "type": "cpt", 
      "size": 1332344
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol10_500ns.xtc"
      }, 
      "checksum": "md5:5a0fa62f3efa7a9037dc6b75c750a85f", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol10_500ns.xtc", 
      "type": "xtc", 
      "size": 1025713704
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol10.edr"
      }, 
      "checksum": "md5:df226f5343e03bfe2297d575fd81c53c", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol10.edr", 
      "type": "edr", 
      "size": 31201356
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol10.gro"
      }, 
      "checksum": "md5:0668733fcb5a08778a252c89329632f3", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol10.gro", 
      "type": "gro", 
      "size": 3824584
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol10.ndx"
      }, 
      "checksum": "md5:593f0567a8b4dd9a8e24d4230e855bbc", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol10.ndx", 
      "type": "ndx", 
      "size": 1305135
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol10.top"
      }, 
      "checksum": "md5:a5c28be711003edae662778efbc74422", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol10.top", 
      "type": "top", 
      "size": 187
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol10.tpr"
      }, 
      "checksum": "md5:efb76b3238320d95adb5ea6486694572", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol10.tpr", 
      "type": "tpr", 
      "size": 1843168
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol10.xtc"
      }, 
      "checksum": "md5:3fd5ee3a8815a856741e14da4e12cbae", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol10.xtc", 
      "type": "xtc", 
      "size": 205305664
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol20_500ns.cpt"
      }, 
      "checksum": "md5:1da6ab1e23407a01b717f3b3fe8f836f", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol20_500ns.cpt", 
      "type": "cpt", 
      "size": 1382072
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol20_500ns.xtc"
      }, 
      "checksum": "md5:a03bd1d3cffd09064ae7b35ed66129b5", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol20_500ns.xtc", 
      "type": "xtc", 
      "size": 1068174512
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol20.edr"
      }, 
      "checksum": "md5:be6eecd2bbee7680db993b8bb85d14df", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol20.edr", 
      "type": "edr", 
      "size": 31201356
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol20.gro"
      }, 
      "checksum": "md5:479aefc0ee0d6dbf77cebdb027e27aaf", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol20.gro", 
      "type": "gro", 
      "size": 3967553
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol20.ndx"
      }, 
      "checksum": "md5:3152b8e302fc9631738343908b8072bd", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol20.ndx", 
      "type": "ndx", 
      "size": 1355415
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol20.top"
      }, 
      "checksum": "md5:edd88e49cddddc146c8e1e95a06f1ad0", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol20.top", 
      "type": "top", 
      "size": 187
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol20.tpr"
      }, 
      "checksum": "md5:a8fc836c726794ec7efb4926be42867e", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol20.tpr", 
      "type": "tpr", 
      "size": 1909472
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol20.xtc"
      }, 
      "checksum": "md5:8d1ec1a27eff11c8714737f181f6f5f8", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol20.xtc", 
      "type": "xtc", 
      "size": 213782584
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol30_500ns.cpt"
      }, 
      "checksum": "md5:9c74bdb00d041fe60ab674011f54363a", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol30_500ns.cpt", 
      "type": "cpt", 
      "size": 1446008
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol30_500ns.xtc"
      }, 
      "checksum": "md5:04e2afa2c4a0b5285339454dd4b782d7", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol30_500ns.xtc", 
      "type": "xtc", 
      "size": 1123757108
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol30.edr"
      }, 
      "checksum": "md5:c47ce43e215633542df396cd13b14345", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol30.edr", 
      "type": "edr", 
      "size": 31201356
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol30.gro"
      }, 
      "checksum": "md5:080e2e5649764dfd80df9b5f16a5fd41", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol30.gro", 
      "type": "gro", 
      "size": 4151359
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol30.ndx"
      }, 
      "checksum": "md5:4f23c039de7518bf88c5ec5e148436bf", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol30.ndx", 
      "type": "ndx", 
      "size": 1420060
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol30.top"
      }, 
      "checksum": "md5:c1d29b98191608457612d0247561e75d", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol30.top", 
      "type": "top", 
      "size": 188
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol30.tpr"
      }, 
      "checksum": "md5:c0a97004d05c3ed9d6aee0abbc7431fe", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol30.tpr", 
      "type": "tpr", 
      "size": 1994720
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/chol30.xtc"
      }, 
      "checksum": "md5:d73840fbec11136de0f51256abf89001", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "chol30.xtc", 
      "type": "xtc", 
      "size": 224921424
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa/md.mdp"
      }, 
      "checksum": "md5:58558e3dcc25460ff5ddb995f0ba9a91", 
      "bucket": "c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
      "key": "md.mdp", 
      "type": "mdp", 
      "size": 1088
    }
  ], 
  "owners": [
    7257
  ], 
  "doi": "10.5281/zenodo.3237420", 
  "stats": {
    "version_unique_downloads": 171.0, 
    "unique_views": 339.0, 
    "views": 410.0, 
    "downloads": 1358.0, 
    "unique_downloads": 129.0, 
    "version_unique_views": 384.0, 
    "volume": 217363723392.0, 
    "version_downloads": 1455.0, 
    "version_views": 498.0, 
    "version_volume": 222071912566.0
  }, 
  "links": {
    "doi": "https://doi.org/10.5281/zenodo.3237420", 
    "conceptdoi": "https://doi.org/10.5281/zenodo.655320", 
    "bucket": "https://zenodo.org/api/files/c919e41d-bf38-4214-b3a2-2d48b2aa49fa", 
    "conceptbadge": "https://zenodo.org/badge/doi/10.5281/zenodo.655320.svg", 
    "html": "https://zenodo.org/record/3237420", 
    "latest_html": "https://zenodo.org/record/3237420", 
    "badge": "https://zenodo.org/badge/doi/10.5281/zenodo.3237420.svg", 
    "latest": "https://zenodo.org/api/records/3237420"
  }, 
  "conceptdoi": "10.5281/zenodo.655320", 
  "created": "2019-06-04T06:51:02.759599+00:00", 
  "updated": "2019-06-04T19:05:39.396850+00:00", 
  "conceptrecid": "655320", 
  "revision": 2, 
  "id": 3237420, 
  "metadata": {
    "access_right_category": "success", 
    "doi": "10.5281/zenodo.3237420", 
    "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": {
      "id": "CC-BY-4.0"
    }, 
    "title": "POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force field.", 
    "relations": {
      "version": [
        {
          "count": 2, 
          "index": 1, 
          "parent": {
            "pid_type": "recid", 
            "pid_value": "655320"
          }, 
          "is_last": true, 
          "last_child": {
            "pid_type": "recid", 
            "pid_value": "3237420"
          }
        }
      ]
    }, 
    "communities": [
      {
        "id": "biophys-uh"
      }, 
      {
        "id": "nmrlipids"
      }, 
      {
        "id": "zenodo"
      }
    ], 
    "publication_date": "2016-10-09", 
    "creators": [
      {
        "orcid": "0000-0003-4858-364X", 
        "affiliation": "TUT", 
        "name": "Javanainen, Matti"
      }
    ], 
    "access_right": "open", 
    "resource_type": {
      "type": "dataset", 
      "title": "Dataset"
    }, 
    "related_identifiers": [
      {
        "scheme": "doi", 
        "relation": "isNewVersionOf", 
        "identifier": "10.5281/zenodo.61649"
      }, 
      {
        "scheme": "doi", 
        "relation": "isVersionOf", 
        "identifier": "10.5281/zenodo.655320"
      }
    ]
  }
}
498
1,455
views
downloads
All versions This version
Views 498410
Downloads 1,4551,358
Data volume 222.1 GB217.4 GB
Unique views 384339
Unique downloads 171129

Share

Cite as