S
Sander Pronk
Researcher at Royal Institute of Technology
Publications - 7
Citations - 6357
Sander Pronk is an academic researcher from Royal Institute of Technology. The author has contributed to research in topics: Massively parallel & Dataflow. The author has an hindex of 7, co-authored 7 publications receiving 5428 citations. Previous affiliations of Sander Pronk include Science for Life Laboratory.
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Journal ArticleDOI
Gromacs 4.5
Sander Pronk,Szilárd Páll,Szilárd Páll,Roland Schulz,Roland Schulz,Per Larsson,Pär Bjelkmar,Pär Bjelkmar,Rossen Apostolov,Rossen Apostolov,Michael R. Shirts,Jeremy C. Smith,Jeremy C. Smith,Peter M. Kasson,David van der Spoel,David van der Spoel,Berk Hess,Berk Hess,Erik Lindahl,Erik Lindahl,Erik Lindahl +20 more
TL;DR: A range of new simulation algorithms and features developed during the past 4 years are presented, leading up to the GROMACS 4.5 software package, which provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.
Gromacs User Manual Version 4.6
E. Apol,Rossen Apostolov,Herman J. C. Berendsen,A. van Buuren,Pär Bjelkmar,R. van Drunen,A. Feenstra,S. Fritsch,Gerrit Groenhof,Christoph Junghans,Peter M. Kasson,Per Larsson,P. Meulenhoff,Teemu Murtola,Szilárd Páll,Sander Pronk,Roland Schulz,Michael R. Shirts,A Sijbers,P. Tieleman,Berk Hess,D. van der Spoel,Erik Lindahl +22 more
Journal ArticleDOI
Dynamic heterogeneity controls diffusion and viscosity near biological interfaces
TL;DR: This work describes how measures developed for studying glassy systems allow quantitative measurement of interfacial effects on water dynamics, showing that correlated motions of particles near a surface result in a viscosity greater than anticipated from individual particle motions.
Journal ArticleDOI
Molecular simulation workflows as parallel algorithms: the execution engine of Copernicus, a distributed high-performance computing platform.
Sander Pronk,Iman Pouya,Magnus Lundborg,Grant M. Rotskoff,Björn Wesén,Peter M. Kasson,Erik Lindahl,Erik Lindahl +7 more
TL;DR: This work describes how the distributed execution framework Copernicus allows the expression of algorithms such as free-energy perturbation, Markov state modeling, metadynamics, or milestoning in generic workflows: dataflow programs and facilitates the optimization of these algorithms with adaptive sampling.
Proceedings ArticleDOI
Copernicus: a new paradigm for parallel adaptive molecular dynamics
Sander Pronk,Gregory R. Bowman,Berk Hess,Per Larsson,Imran S. Haque,Vijay S. Pande,Iman Pouya,Kyle A. Beauchamp,Peter M. Kasson,Erik Lindahl +9 more
TL;DR: A new paradigm for parallel adaptive molecular dynamics and a publicly available implementation: Copernicus, which combines performance-leading molecular dynamics parallelized on three levels (SIMD, threads, and message-passing) with kinetic clustering, statistical model building and real-time result monitoring.