Publikation: A strategy for analysis of (molecular) equilibrium simulations : Configuration space density estimation, clustering, and visualization
Dateien
Datum
Autor:innen
Herausgeber:innen
ISSN der Zeitschrift
Electronic ISSN
ISBN
Bibliografische Daten
Verlag
Schriftenreihe
Auflagebezeichnung
URI (zitierfähiger Link)
DOI (zitierfähiger Link)
Internationale Patentnummer
Link zur Lizenz
Angaben zur Forschungsförderung
Projekt
Open Access-Veröffentlichung
Sammlungen
Core Facility der Universität Konstanz
Titel in einer weiteren Sprache
Publikationstyp
Publikationsstatus
Erschienen in
Zusammenfassung
We propose an approach for summarizing the output of long simulations of complex systems, affording a rapid overview and interpretation. First, multidimensional scaling techniques are used in conjunction with dimension reduction methods to obtain a low-dimensional representation of the configuration space explored by the system. A nonparametric estimate of the density of states in this subspace is then obtained using kernel methods. The free energy surface is calculated from that density, and the configurations produced in the simulation are then clustered according to the topography of that surface, such that all configurations belonging to one local free energy minimum form one class. This topographical cluster analysis is performed using basin spanning trees which we introduce as subgraphs of Delaunay triangulations. Free energy surfaces obtained in dimensions lower than four can be visualized directly using iso-contours and -surfaces. Basin spanning trees also afford a glimpse of higher-dimensional topographies. The procedure is illustrated using molecular dynamics simulations on the reversible folding of peptide analoga. Finally, we emphasize the intimate relation of density estimation techniques to modern enhanced sampling algorithms.
Zusammenfassung in einer weiteren Sprache
Fachgebiet (DDC)
Schlagwörter
Konferenz
Rezension
Zitieren
ISO 690
HAMPRECHT, Fred A., Christine PETER, Xavier DAURA, Walter THIEL, Wilfred F. VAN GUNSTEREN, 2001. A strategy for analysis of (molecular) equilibrium simulations : Configuration space density estimation, clustering, and visualization. In: The Journal of Chemical Physics. 2001, 114(5), pp. 2079-2089. ISSN 0021-9606. eISSN 1089-7690. Available under: doi: 10.1063/1.1330216BibTex
@article{Hamprecht2001-02strat-40245, year={2001}, doi={10.1063/1.1330216}, title={A strategy for analysis of (molecular) equilibrium simulations : Configuration space density estimation, clustering, and visualization}, number={5}, volume={114}, issn={0021-9606}, journal={The Journal of Chemical Physics}, pages={2079--2089}, author={Hamprecht, Fred A. and Peter, Christine and Daura, Xavier and Thiel, Walter and van Gunsteren, Wilfred F.} }
RDF
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:void="http://rdfs.org/ns/void#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > <rdf:Description rdf:about="https://kops.uni-konstanz.de/server/rdf/resource/123456789/40245"> <dc:contributor>Daura, Xavier</dc:contributor> <dc:contributor>Hamprecht, Fred A.</dc:contributor> <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/29"/> <dcterms:title>A strategy for analysis of (molecular) equilibrium simulations : Configuration space density estimation, clustering, and visualization</dcterms:title> <dc:creator>van Gunsteren, Wilfred F.</dc:creator> <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/40245/1/Hamprecht_2-1n64hvixahe787.pdf"/> <foaf:homepage rdf:resource="http://localhost:8080/"/> <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/40245"/> <dc:creator>Thiel, Walter</dc:creator> <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/> <dc:contributor>Thiel, Walter</dc:contributor> <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/40245/1/Hamprecht_2-1n64hvixahe787.pdf"/> <dc:contributor>Peter, Christine</dc:contributor> <dc:creator>Hamprecht, Fred A.</dc:creator> <dcterms:issued>2001-02</dcterms:issued> <dc:creator>Peter, Christine</dc:creator> <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/29"/> <dcterms:rights rdf:resource="https://rightsstatements.org/page/InC/1.0/"/> <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2017-10-05T08:41:42Z</dc:date> <dc:language>eng</dc:language> <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2017-10-05T08:41:42Z</dcterms:available> <dcterms:abstract xml:lang="eng">We propose an approach for summarizing the output of long simulations of complex systems, affording a rapid overview and interpretation. First, multidimensional scaling techniques are used in conjunction with dimension reduction methods to obtain a low-dimensional representation of the configuration space explored by the system. A nonparametric estimate of the density of states in this subspace is then obtained using kernel methods. The free energy surface is calculated from that density, and the configurations produced in the simulation are then clustered according to the topography of that surface, such that all configurations belonging to one local free energy minimum form one class. This topographical cluster analysis is performed using basin spanning trees which we introduce as subgraphs of Delaunay triangulations. Free energy surfaces obtained in dimensions lower than four can be visualized directly using iso-contours and -surfaces. Basin spanning trees also afford a glimpse of higher-dimensional topographies. The procedure is illustrated using molecular dynamics simulations on the reversible folding of peptide analoga. Finally, we emphasize the intimate relation of density estimation techniques to modern enhanced sampling algorithms.</dcterms:abstract> <dc:creator>Daura, Xavier</dc:creator> <dc:contributor>van Gunsteren, Wilfred F.</dc:contributor> <dc:rights>terms-of-use</dc:rights> </rdf:Description> </rdf:RDF>