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Input files for "Faster Simulations with a 5 fs Time Step for Lipids in the CHARMM Force Field"

Karina Olesen; Himanshu Khandelia


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        <foaf:name>Karina Olesen</foaf:name>
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            <foaf:name>MEMPHYS: Center for Biomembrane Physics, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, M 5230 Odense, Denmark</foaf:name>
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        <foaf:name>Himanshu Khandelia</foaf:name>
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            <foaf:name>MEMPHYS: Center for Biomembrane Physics, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, M 5230 Odense, Denmark</foaf:name>
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    <dct:title>Input files for "Faster Simulations with a 5 fs Time Step for Lipids in the CHARMM Force Field"</dct:title>
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    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">2018</dct:issued>
    <dcat:keyword>molecular dynamics simulations, timestep, 5fs, GROMACS, membranes, bilayers, membrane-protein complexes</dcat:keyword>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2018-05-31</dct:issued>
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    <dct:description>&lt;p&gt;The performance of all-atom molecular dynamics simulations is limited by an integration time step of 2 fs, which is needed to resolve the fastest degrees of freedom in the system, namely, the vibration of bonds and angles involving hydrogen atoms. The virtual interaction sites (VIS) method replaces hydrogen atoms by massless virtual interaction sites to eliminate these degrees of freedom while keeping intact nonbonded interactions and the explicit treatment of hydrogen atoms. We have modified the existing VIS algorithm for most lipids in the popular CHARMM36 force field by increasing the hydrogen atom masses at regular intervals in the lipid acyl chains and obtained lipid properties and pore formation free energies in very good agreement with those calculated in simulations without VIS. Our modified VIS scheme enables a 5 fs time step resulting in a significant performance gain for all-atom simulations of membranes. The method has the potential to make longer time and length scales accessible in all-atom simulations of membrane&amp;ndash;protein complexes.&lt;/p&gt; &lt;p&gt;The file set contains individual lipid topologies for virtual interaction sites for standard CHARMM lipids, as well as a README file with instructions on how to implement the VIS algorithm for membranes or membrane-protein complexes&lt;/p&gt; &lt;p&gt;Please Cite:&amp;nbsp;&lt;a href="//pubs.acs.org/doi/10.1021/acs.jctc.8b00267"&gt;10.1021/acs.jctc.8b00267&lt;/a&gt;&lt;/p&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt;</dct:description>
    <dct:description>{"references": ["Olesen K, Awasthi N, Bruhn DS, Pezeshkian W and H Khandelia (2018). JCTC \"Faster Simulations with a 5 fs Time Step for Lipids in the CHARMM Force Field\""]}</dct:description>
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