Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures
Identifieur interne : 000700 ( Main/Exploration ); précédent : 000699; suivant : 000701Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures
Auteurs : John D. Chodera [États-Unis] ; William C. Swope [États-Unis] ; Frank Noé [Allemagne] ; Jan-Hendrik Prinz [Allemagne] ; Michael R. Shirts [États-Unis] ; Vijay S. Pande [États-Unis]Source :
- The Journal of Chemical Physics [ 0021-9606 ] ; 2011.
Abstract
Dynamical averages based on
Url:
DOI: 10.1063/1.3592152
PubMed: 21721612
PubMed Central: 3143679
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000136
- to stream Pmc, to step Curation: 000136
- to stream Pmc, to step Checkpoint: 000514
- to stream Ncbi, to step Merge: 000242
- to stream Ncbi, to step Curation: 000242
- to stream Ncbi, to step Checkpoint: 000242
- to stream Main, to step Merge: 000702
- to stream Main, to step Curation: 000700
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures</title>
<author><name sortKey="Chodera, John D" sort="Chodera, John D" uniqKey="Chodera J" first="John D." last="Chodera">John D. Chodera</name>
<affiliation wicri:level="1"><nlm:aff id="a1">California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, 260J Stanley Hall, Berkeley, California 94720, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, 260J Stanley Hall, Berkeley, California 94720</wicri:regionArea>
<wicri:noRegion>California 94720</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Swope, William C" sort="Swope, William C" uniqKey="Swope W" first="William C." last="Swope">William C. Swope</name>
<affiliation wicri:level="1"><nlm:aff id="a2">IBM Almaden Research Center, San Jose, California 95120, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>IBM Almaden Research Center, San Jose, California 95120</wicri:regionArea>
<wicri:noRegion>California 95120</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Noe, Frank" sort="Noe, Frank" uniqKey="Noe F" first="Frank" last="Noé">Frank Noé</name>
<affiliation wicri:level="3"><nlm:aff id="a3">DFG Research Center Matheon, FU Berlin, Arnimallee 6, 14195 Berlin, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>DFG Research Center Matheon, FU Berlin, Arnimallee 6, 14195 Berlin</wicri:regionArea>
<placeName><region type="land" nuts="3">Berlin</region>
<settlement type="city">Berlin</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Prinz, Jan Hendrik" sort="Prinz, Jan Hendrik" uniqKey="Prinz J" first="Jan-Hendrik" last="Prinz">Jan-Hendrik Prinz</name>
<affiliation wicri:level="3"><nlm:aff id="a3">DFG Research Center Matheon, FU Berlin, Arnimallee 6, 14195 Berlin, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>DFG Research Center Matheon, FU Berlin, Arnimallee 6, 14195 Berlin</wicri:regionArea>
<placeName><region type="land" nuts="3">Berlin</region>
<settlement type="city">Berlin</settlement>
</placeName>
</affiliation>
<affiliation wicri:level="3"><nlm:aff id="a4">IWR, University of Heidelberg, INF 368, 69120 Heidelberg, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>IWR, University of Heidelberg, INF 368, 69120 Heidelberg</wicri:regionArea>
<placeName><region type="land" nuts="1">Bade-Wurtemberg</region>
<region type="district" nuts="2">District de Karlsruhe</region>
<settlement type="city">Heidelberg</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Shirts, Michael R" sort="Shirts, Michael R" uniqKey="Shirts M" first="Michael R." last="Shirts">Michael R. Shirts</name>
<affiliation wicri:level="1"><nlm:aff id="a5">Department of Chemical Engineering, University of Virginia, Virginia 22904, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemical Engineering, University of Virginia, Virginia 22904</wicri:regionArea>
<wicri:noRegion>Virginia 22904</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Pande, Vijay S" sort="Pande, Vijay S" uniqKey="Pande V" first="Vijay S." last="Pande">Vijay S. Pande</name>
<affiliation wicri:level="1"><nlm:aff id="a6">Department of Chemistry, Stanford University, Stanford, California 94305, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemistry, Stanford University, Stanford, California 94305</wicri:regionArea>
<wicri:noRegion>California 94305</wicri:noRegion>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">21721612</idno>
<idno type="pmc">3143679</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143679</idno>
<idno type="RBID">PMC:3143679</idno>
<idno type="doi">10.1063/1.3592152</idno>
<date when="2011">2011</date>
<idno type="wicri:Area/Pmc/Corpus">000136</idno>
<idno type="wicri:Area/Pmc/Curation">000136</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000514</idno>
<idno type="wicri:Area/Ncbi/Merge">000242</idno>
<idno type="wicri:Area/Ncbi/Curation">000242</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">000242</idno>
<idno type="wicri:doubleKey">0021-9606:2011:Chodera J:dynamical:reweighting:improved</idno>
<idno type="wicri:Area/Main/Merge">000702</idno>
<idno type="wicri:Area/Main/Curation">000700</idno>
<idno type="wicri:Area/Main/Exploration">000700</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures</title>
<author><name sortKey="Chodera, John D" sort="Chodera, John D" uniqKey="Chodera J" first="John D." last="Chodera">John D. Chodera</name>
<affiliation wicri:level="1"><nlm:aff id="a1">California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, 260J Stanley Hall, Berkeley, California 94720, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, 260J Stanley Hall, Berkeley, California 94720</wicri:regionArea>
<wicri:noRegion>California 94720</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Swope, William C" sort="Swope, William C" uniqKey="Swope W" first="William C." last="Swope">William C. Swope</name>
<affiliation wicri:level="1"><nlm:aff id="a2">IBM Almaden Research Center, San Jose, California 95120, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>IBM Almaden Research Center, San Jose, California 95120</wicri:regionArea>
<wicri:noRegion>California 95120</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Noe, Frank" sort="Noe, Frank" uniqKey="Noe F" first="Frank" last="Noé">Frank Noé</name>
<affiliation wicri:level="3"><nlm:aff id="a3">DFG Research Center Matheon, FU Berlin, Arnimallee 6, 14195 Berlin, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>DFG Research Center Matheon, FU Berlin, Arnimallee 6, 14195 Berlin</wicri:regionArea>
<placeName><region type="land" nuts="3">Berlin</region>
<settlement type="city">Berlin</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Prinz, Jan Hendrik" sort="Prinz, Jan Hendrik" uniqKey="Prinz J" first="Jan-Hendrik" last="Prinz">Jan-Hendrik Prinz</name>
<affiliation wicri:level="3"><nlm:aff id="a3">DFG Research Center Matheon, FU Berlin, Arnimallee 6, 14195 Berlin, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>DFG Research Center Matheon, FU Berlin, Arnimallee 6, 14195 Berlin</wicri:regionArea>
<placeName><region type="land" nuts="3">Berlin</region>
<settlement type="city">Berlin</settlement>
</placeName>
</affiliation>
<affiliation wicri:level="3"><nlm:aff id="a4">IWR, University of Heidelberg, INF 368, 69120 Heidelberg, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>IWR, University of Heidelberg, INF 368, 69120 Heidelberg</wicri:regionArea>
<placeName><region type="land" nuts="1">Bade-Wurtemberg</region>
<region type="district" nuts="2">District de Karlsruhe</region>
<settlement type="city">Heidelberg</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Shirts, Michael R" sort="Shirts, Michael R" uniqKey="Shirts M" first="Michael R." last="Shirts">Michael R. Shirts</name>
<affiliation wicri:level="1"><nlm:aff id="a5">Department of Chemical Engineering, University of Virginia, Virginia 22904, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemical Engineering, University of Virginia, Virginia 22904</wicri:regionArea>
<wicri:noRegion>Virginia 22904</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Pande, Vijay S" sort="Pande, Vijay S" uniqKey="Pande V" first="Vijay S." last="Pande">Vijay S. Pande</name>
<affiliation wicri:level="1"><nlm:aff id="a6">Department of Chemistry, Stanford University, Stanford, California 94305, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemistry, Stanford University, Stanford, California 94305</wicri:regionArea>
<wicri:noRegion>California 94305</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">The Journal of Chemical Physics</title>
<idno type="ISSN">0021-9606</idno>
<idno type="eISSN">1089-7690</idno>
<imprint><date when="2011">2011</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>Dynamical averages based on <italic>functionals</italic>
of dynamical trajectories, such as time-correlation functions, play an important role in determining kinetic or transport properties of matter. At temperatures of interest, the expectations of these quantities are often dominated by contributions from rare events, making the precise calculation of these quantities by molecular dynamics simulation difficult. Here, we present a reweighting method for combining simulations from multiple temperatures (or from simulated or parallel tempering simulations) to compute an optimal estimate of the dynamical properties at the temperature of interest without the need to invoke an approximate kinetic model (such as the Arrhenius law). Continuous and differentiable estimates of these expectations at any temperature in the sampled range can also be computed, along with an assessment of the associated statistical uncertainty. For rare events, aggregating data from multiple temperatures can produce an estimate with the desired precision at greatly reduced computational cost compared with simulations conducted at a single temperature. Here, we describe use of the method for the canonical (NVT) ensemble using four common models of dynamics (canonical distribution of Hamiltonian trajectories, Andersen thermostatting, Langevin, and overdamped Langevin or Brownian dynamics), but it can be applied to <italic>any</italic>
thermodynamic ensemble provided the ratio of path probabilities at different temperatures can be computed. To illustrate the method, we compute a time-correlation function for solvated terminally-blocked alanine peptide across a range of temperatures using trajectories harvested using a modified parallel tempering protocol.</p>
</div>
</front>
</TEI>
<affiliations><list><country><li>Allemagne</li>
<li>États-Unis</li>
</country>
<region><li>Bade-Wurtemberg</li>
<li>Berlin</li>
<li>District de Karlsruhe</li>
</region>
<settlement><li>Berlin</li>
<li>Heidelberg</li>
</settlement>
</list>
<tree><country name="États-Unis"><noRegion><name sortKey="Chodera, John D" sort="Chodera, John D" uniqKey="Chodera J" first="John D." last="Chodera">John D. Chodera</name>
</noRegion>
<name sortKey="Pande, Vijay S" sort="Pande, Vijay S" uniqKey="Pande V" first="Vijay S." last="Pande">Vijay S. Pande</name>
<name sortKey="Shirts, Michael R" sort="Shirts, Michael R" uniqKey="Shirts M" first="Michael R." last="Shirts">Michael R. Shirts</name>
<name sortKey="Swope, William C" sort="Swope, William C" uniqKey="Swope W" first="William C." last="Swope">William C. Swope</name>
</country>
<country name="Allemagne"><region name="Berlin"><name sortKey="Noe, Frank" sort="Noe, Frank" uniqKey="Noe F" first="Frank" last="Noé">Frank Noé</name>
</region>
<name sortKey="Prinz, Jan Hendrik" sort="Prinz, Jan Hendrik" uniqKey="Prinz J" first="Jan-Hendrik" last="Prinz">Jan-Hendrik Prinz</name>
<name sortKey="Prinz, Jan Hendrik" sort="Prinz, Jan Hendrik" uniqKey="Prinz J" first="Jan-Hendrik" last="Prinz">Jan-Hendrik Prinz</name>
</country>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000700 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000700 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Ticri/CIDE |area= CyberinfraV1 |flux= Main |étape= Exploration |type= RBID |clé= PMC:3143679 |texte= Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:21721612" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \ | NlmPubMed2Wicri -a CyberinfraV1
This area was generated with Dilib version V0.6.25. |