JGromacs: A Java Package for Analyzing Protein Simulations

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. Availability: JGromacs
and detailed documentation is freely available from http://sbcb.bioch.ox.ac.uk/jgromacs
under a GPLv3 license.