GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
Top Cited Papers
Open Access
- 13 February 2013
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 29 (7) , 845-854
- https://doi.org/10.1093/bioinformatics/btt055
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 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. Contact:erik.lindahl@scilifelab.se Supplementary information: Supplementary data are available at Bioinformatics online.Keywords
This publication has 50 references indexed in Scilit:
- Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric ConstantJournal of Chemical Theory and Computation, 2011
- Atomistic Folding Simulations of the Five-Helix Bundle Protein λ6−85Journal of the American Chemical Society, 2010
- Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding SiteJournal of Molecular Biology, 2009
- CHARMM: The biomolecular simulation programJournal of Computational Chemistry, 2009
- Scalable Algorithms for Molecular Dynamics Simulations on Commodity ClustersPublished by Institute of Electrical and Electronics Engineers (IEEE) ,2006
- The GROMOS software for biomolecular simulation: GROMOS05Journal of Computational Chemistry, 2005
- The Amber biomolecular simulation programsJournal of Computational Chemistry, 2005
- Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7Proceedings of the National Academy of Sciences, 1999
- Efficient estimation of free energy differences from Monte Carlo dataJournal of Computational Physics, 1976
- Phase Transition for a Hard Sphere SystemThe Journal of Chemical Physics, 1957