title: GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  GROMACS is an open source and free software available from http://www.gromacs.org.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden.
authors: Sander
authors: S
authors: Pronk
authors: Szilárd
authors: S
authors: Páll
authors: Roland
authors: R
authors: Schulz
authors: Per
authors: P
authors: Larsson
authors: Pär
authors: P
authors: Bjelkmar
authors: Rossen
authors: R
authors: Apostolov
authors: Michael R
authors: MR
authors: Shirts
authors: Jeremy C
authors: JC
authors: Smith
authors: Peter M
authors: PM
authors: Kasson
authors: David
authors: D
authors: van der Spoel
authors: Berk
authors: B
authors: Hess
authors: Erik
authors: E
authors: Lindahl
mesh_terms: D000465:Algorithms; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry; D012984:Software
chemical_list: D011506:Proteins