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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Rapid Exploration of Configuration Space with Diffusion Map-directed-Molecular Dynamics</title><author><name sortKey="Zheng, Wenwei" sort="Zheng, Wenwei" uniqKey="Zheng W" first="Wenwei" last="Zheng">Wenwei Zheng</name></author><author><name sortKey="Rohrdanz, Mary A" sort="Rohrdanz, Mary A" uniqKey="Rohrdanz M" first="Mary A." last="Rohrdanz">Mary A. Rohrdanz</name></author><author><name sortKey="Clementi, Cecilia" sort="Clementi, Cecilia" uniqKey="Clementi C" first="Cecilia" last="Clementi">Cecilia Clementi</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23865517</idno><idno type="pmc">3808479</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3808479</idno><idno type="RBID">PMC:3808479</idno><idno type="doi">10.1021/jp401911h</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000429</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Rapid Exploration of Configuration Space with Diffusion Map-directed-Molecular Dynamics</title><author><name sortKey="Zheng, Wenwei" sort="Zheng, Wenwei" uniqKey="Zheng W" first="Wenwei" last="Zheng">Wenwei Zheng</name></author><author><name sortKey="Rohrdanz, Mary A" sort="Rohrdanz, Mary A" uniqKey="Rohrdanz M" first="Mary A." last="Rohrdanz">Mary A. Rohrdanz</name></author><author><name sortKey="Clementi, Cecilia" sort="Clementi, Cecilia" uniqKey="Clementi C" first="Cecilia" last="Clementi">Cecilia Clementi</name></author></analytic><series><title level="j">The journal of physical chemistry. B</title><idno type="ISSN">1520-6106</idno><idno type="eISSN">1520-5207</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">The gap between the timescale of interesting behavior in macromolecular systems and that which our computational resources can afford oftentimes limits Molecular Dynamics (MD) from understanding experimental results and predicting what is inaccessible in experiments. In this paper, we introduce a new sampling scheme, named Diffusion Map-directed-MD (DM-d-MD), to rapidly explore molecular configuration space. The method uses diffusion map to guide MD on the fly. DM-d-MD can be combined with other methods to reconstruct the equilibrium free energy, and here we used umbrella sampling as an example. We present results from two systems: alanine dipeptide and alanine-12. In both systems we gain tremendous speedup with respect to standard MD both in exploring the configuration space and reconstructing the equilibrium distribution. In particular, we obtain 3 orders of magnitude of speedup over standard MD in the exploration of the configurational space of alanine-12 at 300K with DM-d-MD. The method is reaction coordinate free and minimally dependent on a priori knowledge of the system. We expect wide applications of DM-d-MD to other macromolecular systems in which equilibrium sampling is not affordable by standard MD.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
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<front><journal-meta><journal-id journal-id-type="nlm-journal-id">101157530</journal-id><journal-id journal-id-type="pubmed-jr-id">30073</journal-id><journal-id journal-id-type="nlm-ta">J Phys Chem B</journal-id><journal-id journal-id-type="iso-abbrev">J Phys Chem B</journal-id><journal-title-group><journal-title>The journal of physical chemistry. B</journal-title></journal-title-group><issn pub-type="ppub">1520-6106</issn><issn pub-type="epub">1520-5207</issn></journal-meta><article-meta><article-id pub-id-type="pmid">23865517</article-id><article-id pub-id-type="pmc">3808479</article-id><article-id pub-id-type="doi">10.1021/jp401911h</article-id><article-id pub-id-type="manuscript">NIHMS513908</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Rapid Exploration of Configuration Space with Diffusion Map-directed-Molecular Dynamics</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Zheng</surname><given-names>Wenwei</given-names></name></contrib><contrib contrib-type="author"><name><surname>Rohrdanz</surname><given-names>Mary A.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Clementi</surname><given-names>Cecilia</given-names></name><xref rid="FN1" ref-type="author-notes">*</xref></contrib><aff id="A1">Department of Chemistry, Rice University, Houston TX 77005</aff></contrib-group><author-notes><corresp id="FN1"><label>*</label>To whom correspondence should be addressed: <email>cecilia@rice.edu</email>, Phone: 713 3483485. Fax: 713 3483485</corresp></author-notes><pub-date pub-type="nihms-submitted"><day>21</day><month>9</month><year>2013</year></pub-date><pub-date pub-type="epub"><day>07</day><month>8</month><year>2013</year></pub-date><pub-date pub-type="ppub"><day>24</day><month>10</month><year>2013</year></pub-date><pub-date pub-type="pmc-release"><day>24</day><month>10</month><year>2014</year></pub-date><volume>117</volume><issue>42</issue><elocation-id>10.1021/jp401911h</elocation-id><abstract><p id="P1">The gap between the timescale of interesting behavior in macromolecular systems and that which our computational resources can afford oftentimes limits Molecular Dynamics (MD) from understanding experimental results and predicting what is inaccessible in experiments. In this paper, we introduce a new sampling scheme, named Diffusion Map-directed-MD (DM-d-MD), to rapidly explore molecular configuration space. The method uses diffusion map to guide MD on the fly. DM-d-MD can be combined with other methods to reconstruct the equilibrium free energy, and here we used umbrella sampling as an example. We present results from two systems: alanine dipeptide and alanine-12. In both systems we gain tremendous speedup with respect to standard MD both in exploring the configuration space and reconstructing the equilibrium distribution. In particular, we obtain 3 orders of magnitude of speedup over standard MD in the exploration of the configurational space of alanine-12 at 300K with DM-d-MD. The method is reaction coordinate free and minimally dependent on a priori knowledge of the system. We expect wide applications of DM-d-MD to other macromolecular systems in which equilibrium sampling is not affordable by standard MD.</p></abstract><kwd-group><kwd>diffusion map</kwd><kwd>molecular dynamics</kwd><kwd>umbrella sampling</kwd></kwd-group><funding-group><award-group><funding-source country="United States">National Center for Research Resources : NCRR</funding-source><award-id>S10 RR029501 || RR</award-id></award-group></funding-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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