Interactive Molecular Dynamics: Scaling up to Large Systems
DREHER, Matthieu
PrograMming and scheduling design fOr Applications in Interactive Simulation [MOAIS]
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PrograMming and scheduling design fOr Applications in Interactive Simulation [MOAIS]
DREHER, Matthieu
PrograMming and scheduling design fOr Applications in Interactive Simulation [MOAIS]
PrograMming and scheduling design fOr Applications in Interactive Simulation [MOAIS]
CHAVENT, Matthieu
Quality control and dynamic reliability [CQFD]
Institut de Mathématiques de Bordeaux [IMB]
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Quality control and dynamic reliability [CQFD]
Institut de Mathématiques de Bordeaux [IMB]
Langue
en
Article de revue
Ce document a été publié dans
Procedia Computer Science. 2013, vol. 18, p. 20-29
Elsevier
Résumé en anglais
Combining 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 ...Lire la suite >
Combining 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.< Réduire
Mots clés en anglais
Interactive Molecular Dynamics
Computational Steering with Haptic Arm
High Performance Interactive Computing
Origine
Importé de halUnités de recherche