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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  <identifier identifierType="DOI">10.5281/zenodo.3237420</identifier>
  <creators>
    <creator>
      <creatorName>Javanainen, Matti</creatorName>
      <givenName>Matti</givenName>
      <familyName>Javanainen</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-4858-364X</nameIdentifier>
      <affiliation>TUT</affiliation>
    </creator>
  </creators>
  <titles>
    <title>POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force field.</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2016</publicationYear>
  <dates>
    <date dateType="Issued">2016-10-09</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3237420</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsNewVersionOf">10.5281/zenodo.61649</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.655320</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/biophys-uh</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/nmrlipids</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/zenodo</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="http://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;A POPC bilayer consisting of 200 lipids (100 per leaflet)&amp;nbsp;is simulated in the presence of 0% (0 molecules), 10 %&amp;nbsp;(22 molecules), 20 % (50 molecules), or 30 % (86 molecules)&amp;nbsp;of cholesterol.&amp;nbsp;The Charmm36&amp;nbsp;model [1] is employed for lipids and the Charmm-compatible variant&amp;nbsp;of the tip3p model for water.&lt;/p&gt;

&lt;p&gt;The Charmm36 force field parameters were obtained from CHARMM-GUI [2] at http://www.charmm-gui.org&lt;/p&gt;

&lt;p&gt;*** IMPORTANT&amp;nbsp;***&lt;/p&gt;

&lt;p&gt;This is a correction to an earlier dataset simulated with some missing dihedrals, see:&amp;nbsp;DOI: 10.5281/zenodo.61649&lt;/p&gt;

&lt;p&gt;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&lt;/p&gt;

&lt;p&gt;The files are in GROMACS format. Trajectory (.xtc) is&amp;nbsp;100 ns long with data saved every 100 ps. Additionally, the initial&amp;nbsp;structure (.gro), topology (.top), index file (.ndx), simulation paremeter file (.mdp), binary run input file&amp;nbsp;for GROMACS v. 5.0&amp;ndash;&amp;gt; (.tpr) and the energy output file&amp;nbsp;(.edr) are provided.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;UPDATE: Longer 500 ns&amp;nbsp;trajectories are updated together with the checkpoint files.&lt;/p&gt;

&lt;p&gt;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&amp;ndash;&lt;/p&gt;

&lt;p&gt;[1] Update of the CHARMM All-Atom Additive Force Field&amp;nbsp;for Lipids:&amp;nbsp;Validation on Six Lipid Types&lt;/p&gt;

&lt;p&gt;Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, &amp;nbsp;Joseph W. O&amp;rsquo;Connor,&amp;nbsp;Douglas J. Tobias, Carlos Mondragon-Ramirez,&amp;nbsp;Igor Vorobyov, Alexander D.&amp;nbsp;MacKerell, Jr., and Richard W. Pastor&lt;/p&gt;

&lt;p&gt;The Journal of Physical Chemistry B 2010 114 (23), 7830-7843&lt;/p&gt;

&lt;p&gt;DOI: 10.1021/jp101759q&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;[2] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM,&amp;nbsp;and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field&lt;/p&gt;

&lt;p&gt;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,&amp;nbsp;Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III,&amp;nbsp;Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im&lt;/p&gt;

&lt;p&gt;Journal of Chemical Theory and Computation 2016 12 (1), 405-413&lt;/p&gt;

&lt;p&gt;DOI: 10.1021/acs.jctc.5b00935&lt;/p&gt;</description>
  </descriptions>
</resource>
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