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Interactive Molecular Dynamics: Scaling up to Large Systems

hal.structure.identifierPrograMming and scheduling design fOr Applications in Interactive Simulation [MOAIS]
dc.contributor.authorDREHER, Matthieu
hal.structure.identifierAlgorithms for Modeling and Simulation of Nanosystems [NANO-D]
dc.contributor.authorPIUZZI, Marc
hal.structure.identifierLaboratoire d'Informatique Fondamentale d'Orléans [LIFO]
dc.contributor.authorTURKI, Ahmed
hal.structure.identifierQuality control and dynamic reliability [CQFD]
hal.structure.identifierInstitut de Mathématiques de Bordeaux [IMB]
dc.contributor.authorCHAVENT, Matthieu
hal.structure.identifierLaboratoire de biochimie théorique [Paris] [LBT (UPR_9080)]
dc.contributor.authorBAADEN, Marc
hal.structure.identifierLaboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur [LIMSI]
dc.contributor.authorFÉREY, Nicolas
hal.structure.identifierLaboratoire d'Informatique Fondamentale d'Orléans [LIFO]
dc.contributor.authorLIMET, Sébastien
hal.structure.identifierPrograMming and scheduling design fOr Applications in Interactive Simulation [MOAIS]
dc.contributor.authorRAFFIN, Bruno
hal.structure.identifierLaboratoire d'Informatique Fondamentale d'Orléans [LIFO]
dc.contributor.authorROBERT, Sophie
dc.date.accessioned2024-04-04T03:20:08Z
dc.date.available2024-04-04T03:20:08Z
dc.date.issued2013
dc.identifier.issn1877-0509
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/194566
dc.description.abstractEnCombining molecular dynamics simulations with user interaction would have various applications in both education and research. By enabling interactivity the scientist will be able to visualize the experiment in real time and drive the simulation to a desired state more easily. However, interacting with systems of interesting size requires significant computing resources due to the complexity of the simulation. In this paper, we propose an approach to combine a classical parallel molecular dynamics simulator, Gromacs, to a 3D virtual reality environment allowing to steer the simulation through external user forces applied with an haptic device to a selection of atoms. We specifically focused on minimizing the intrusion in the simulator code, on efficient parallel data extraction and filtering to transfer only the necessary data to the visualization environment, and on a controlled asynchronism between various components to improve interactivity. We managed to steer molecular systems of 1.7 M atoms at about 25 Hz using 384 CPU cores. This framework allowed us to study a concrete scientific problem by testing one hypothesis of the transport of an iron complex from the exterior of the bacteria to the periplasmic space through the FepA membrane protein.
dc.language.isoen
dc.publisherElsevier
dc.subject.enInteractive Molecular Dynamics
dc.subject.enComputational Steering with Haptic Arm
dc.subject.enHigh Performance Interactive Computing
dc.title.enInteractive Molecular Dynamics: Scaling up to Large Systems
dc.typeArticle de revue
dc.identifier.doi10.1016/j.procs.2013.05.165
dc.subject.halInformatique [cs]/Calcul parallèle, distribué et partagé [cs.DC]
bordeaux.journalProcedia Computer Science
bordeaux.page20-29
bordeaux.volume18
bordeaux.hal.laboratoriesInstitut de Mathématiques de Bordeaux (IMB) - UMR 5251*
bordeaux.institutionUniversité de Bordeaux
bordeaux.institutionBordeaux INP
bordeaux.institutionCNRS
bordeaux.peerReviewedoui
hal.identifierhal-01084652
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-01084652v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Procedia%20Computer%20Science&rft.date=2013&rft.volume=18&rft.spage=20-29&rft.epage=20-29&rft.eissn=1877-0509&rft.issn=1877-0509&rft.au=DREHER,%20Matthieu&PIUZZI,%20Marc&TURKI,%20Ahmed&CHAVENT,%20Matthieu&BAADEN,%20Marc&rft.genre=article


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