GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
Sander Pronk1 Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden, 2Theoretical and Computational Biophysics, Dept. Theoretical Physics, KTH Royal Institute of Technology, 10691 Stockholm, Sweden, 3UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA, 4Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA, 5Department of Molecular Physiology and Biological Physics, 6Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA, 7Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden, 8Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA and 9Department of Cell and Molecular Biology, Uppsala University, Uppsala, SwedenSzilárd Páll1 Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden, 2Theoretical and Computational Biophysics, Dept. Theoretical Physics, KTH Royal Institute of Technology, 10691 Stockholm, Sweden, 3UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA, 4Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA, 5Department of Molecular Physiology and Biological Physics, 6Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA, 7Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden, 8Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA and 9Department of Cell and Molecular Biology, Uppsala University, Uppsala, SwedenRoland Schulz1 Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden, 2Theoretical and Computational Biophysics, Dept. Theoretical Physics, KTH Royal Institute of Technology, 10691 Stockholm, Sweden, 3UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA, 4Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA, 5Department of Molecular Physiology and Biological Physics, 6Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA, 7Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden, 8Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA and 9Department of Cell and Molecular Biology, Uppsala University, Uppsala, SwedenPer Larsson1 Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden, 2Theoretical and Computational Biophysics, Dept. Theoretical Physics, KTH Royal Institute of Technology, 10691 Stockholm, Sweden, 3UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA, 4Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA, 5Department of Molecular Physiology and Biological Physics, 6Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA, 7Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden, 8Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA and 9Department of Cell and Molecular Biology, Uppsala University, Uppsala, SwedenPär BjelkmarStockholm UniversityRossen Apostolov1 Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden, 2Theoretical and Computational Biophysics, Dept. Theoretical Physics, KTH Royal Institute of Technology, 10691 Stockholm, Sweden, 3UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA, 4Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA, 5Department of Molecular Physiology and Biological Physics, 6Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA, 7Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden, 8Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA and 9Department of Cell and Molecular Biology, Uppsala University, Uppsala, SwedenMichael R. Shirts1 Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden, 2Theoretical and Computational Biophysics, Dept. Theoretical Physics, KTH Royal Institute of Technology, 10691 Stockholm, Sweden, 3UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA, 4Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA, 5Department of Molecular Physiology and Biological Physics, 6Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA, 7Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden, 8Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA and 9Department of Cell and Molecular Biology, Uppsala University, Uppsala, SwedenJeremy C. Smith1 Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden, 2Theoretical and Computational Biophysics, Dept. Theoretical Physics, KTH Royal Institute of Technology, 10691 Stockholm, Sweden, 3UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA, 4Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA, 5Department of Molecular Physiology and Biological Physics, 6Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA, 7Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden, 8Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA and 9Department of Cell and Molecular Biology, Uppsala University, Uppsala, SwedenPeter M. KassonStockholm UniversityDavid van der Spoel1 Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden, 2Theoretical and Computational Biophysics, Dept. Theoretical Physics, KTH Royal Institute of Technology, 10691 Stockholm, Sweden, 3UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA, 4Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA, 5Department of Molecular Physiology and Biological Physics, 6Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA, 7Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden, 8Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA and 9Department of Cell and Molecular Biology, Uppsala University, Uppsala, SwedenBerk Hess1 Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden, 2Theoretical and Computational Biophysics, Dept. Theoretical Physics, KTH Royal Institute of Technology, 10691 Stockholm, Sweden, 3UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA, 4Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA, 5Department of Molecular Physiology and Biological Physics, 6Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA, 7Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden, 8Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA and 9Department of Cell and Molecular Biology, Uppsala University, Uppsala, SwedenErik Lindahl1 Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden, 2Theoretical and Computational Biophysics, Dept. Theoretical Physics, KTH Royal Institute of Technology, 10691 Stockholm, Sweden, 3UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA, 4Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA, 5Department of Molecular Physiology and Biological Physics, 6Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA, 7Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden, 8Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA and 9Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
2013en
ABI
Аннотация
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 algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations. AVAILABILITY: GROMACS is an open source and free software available from http://www.gromacs.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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