title: JGromacs: a Java package for analyzing protein simulations.
abstract: In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds on the strengths of object-oriented programming in Java by providing a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure, and dynamics information. The easy-to-learn, easy-to-use, and easy-to-extend framework is intended to simplify and accelerate the implementation and development of complex data analysis algorithms. Furthermore, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g., XML-based configuration) to create applications with a user interface resembling the command-line interface of GROMACS applications.
  
  
  BACKGROUND
  JGromacs and detailed documentation is freely available from  http://sbcb.bioch.ox.ac.uk/jgromacs under a GPLv3 license .
authors.affiliation: Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
authors.forename: Márton
authors.initials: M
authors.lastname: Münz
authors.forename: Philip C
authors.initials: PC
authors.lastname: Biggin
mesh_terms: D000465:Algorithms; D000818:Animals; D004331:Drosophila melanogaster; D006801:Humans; D056004:Molecular Dynamics Simulation; D011381:Programming Languages; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins