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POPC @ 310K, varying amounts of NaCl. Model by Maciejewski and Rog

Javanainen, Matti; Tynkkynen, Joona


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  <identifier identifierType="DOI">10.5281/zenodo.14976</identifier>
  <creators>
    <creator>
      <creatorName>Javanainen, Matti</creatorName>
      <givenName>Matti</givenName>
      <familyName>Javanainen</familyName>
      <affiliation>TUT</affiliation>
    </creator>
    <creator>
      <creatorName>Tynkkynen, Joona</creatorName>
      <givenName>Joona</givenName>
      <familyName>Tynkkynen</familyName>
      <affiliation>TUT</affiliation>
    </creator>
  </creators>
  <titles>
    <title>POPC @ 310K, varying amounts of NaCl. Model by Maciejewski and Rog</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2015</publicationYear>
  <dates>
    <date dateType="Issued">2015-02-10</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://sandbox.zenodo.org/record/14976</alternateIdentifier>
  </alternateIdentifiers>
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  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="http://creativecommons.org/publicdomain/zero/1.0/legalcode">Creative Commons Zero v1.0 Universal</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;Input parameter files and parts of the resulting trajectories&amp;nbsp;for a POPC bilayer simulation with varying amounts of NaCl. The systems contain 100, 200, 300 or 400mM NaCl.&amp;nbsp;The force field is an extension to the OPLS-based force field by the same authors&amp;nbsp;[1]. The data for the salt-free system is available at&amp;nbsp;http://dx.doi.org/10.5281/zenodo.13498&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;&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;Files:&lt;/p&gt;

&lt;p&gt;XXmM_50ns_100ps.xtc &amp;ndash; XX mM&amp;nbsp;NaCl;&amp;nbsp;The last 50 ns of a 90 ns long simulation (40 ns discarded from the beginning). Data saved every 100 ps.&lt;/p&gt;

&lt;p&gt;XX.tpr &amp;ndash; XX mM NaCl. The run input file for Gromacs versions 4.5&amp;nbsp;and above.&amp;nbsp;&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;&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;This data is used in the project &amp;quot;Matching lipid force fields with NMR data&amp;quot;, see:&amp;nbsp;http://nmrlipids.blogspot.fi and referred to in the blog as &amp;#39;MacRog&amp;#39;&lt;/p&gt;

&lt;p&gt;[1] Maciejewski, A., Pasenkiewicz-Gierula, M., Cramariuc, O., Vattulainen, I., and Rog, T.&amp;nbsp;&lt;strong&gt;Refined OPLS All-Atom Force Field for Saturated Phosphatidylcholine Bilayers at Full Hydration.&lt;/strong&gt;&amp;nbsp;The Journal of Physical Chemistry B&amp;nbsp;&lt;strong&gt;118&lt;/strong&gt;, 4571&amp;ndash;4581 (2014). DOI:&amp;nbsp;10.1021/jp5016627&lt;/p&gt;</description>
  </descriptions>
</resource>
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