Multiscaling algorithms for molecular dynamics simulations with GROMACS

This article presents the parallel implementation of a new multiscale model that is currently developed in the Molecular Dynamics Group from the University of Groningen. Multiscale methods combine the advantages of two levels of simulation, an atomistic and a coarse-grain one, with a small loss of p...

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Bibliographic Details
Main Authors: Goga, N., Marrink, S., Costache, S.V., Moldoveanu, F.
Format: Conference Proceeding
Language:English
Subjects:
Algorithm design and analysis
Computational modeling
Computer science
Computer simulation
Equations
Heuristic algorithms
Parallel algorithms
Performance loss
Proteins
Prototypes
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Summary:This article presents the parallel implementation of a new multiscale model that is currently developed in the Molecular Dynamics Group from the University of Groningen. Multiscale methods combine the advantages of two levels of simulation, an atomistic and a coarse-grain one, with a small loss of performance. We designed a parallel implementation of this multiscale approach based on the improved parallel algorithms from the GROMACS MD simulator. The properties of the simulated systems were undisturbed and the errors were kept to a minimum. By having a parallel multiscale simulation, one can take advantage of a reduced simulation time by running it on multiple processors, and in the same time, access to both atomistic and macroscopic details is offered for a better understanding of the desired phenomenon.
DOI:10.1109/SYSTEMS.2009.4815825