GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
Oak Ridge National Laboratory · Stockholm University · +4 more institutions
Abstract
MOTIVATION: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. RESULTS: Here, we present a range of new simulation…
Citation impact
- FWCI
- 268.90
- Percentile
- 100%
- References
- 53
Authors
12- SPSander Pronk
Oak Ridge National Laboratory, Stockholm University, Science for Life Laboratory, University of Virginia, University of Tennessee at Knoxville, KTH Royal Institute of Technology
- SPSzilárd Páll
Oak Ridge National Laboratory, Stockholm University, Science for Life Laboratory, University of Virginia, University of Tennessee at Knoxville, KTH Royal Institute of Technology
- RSRoland Schulz
Oak Ridge National Laboratory, Stockholm University, Science for Life Laboratory, University of Virginia, University of Tennessee at Knoxville, KTH Royal Institute of Technology
- PLPer Larsson
Oak Ridge National Laboratory, Stockholm University, Science for Life Laboratory, University of Virginia, University of Tennessee at Knoxville, KTH Royal Institute of Technology
- PBPär Bjelkmar
Oak Ridge National Laboratory, Stockholm University, Science for Life Laboratory, University of Virginia, University of Tennessee at Knoxville, KTH Royal Institute of Technology
Topics & keywords
- Computer science
- Massively parallel
- Software
- Throughput
- Computational science
- Multithreading
- Parallel computing
- Workstation
- Affordable and clean energy