Note: JGromacs is no longer supported or maintained. The information is provided here for archive purposes.
What is JGromacs?
JGromacs is a Java library designed to facilitate the development of cross-platform analysis applications for Molecular Dynamics (MD) simulations. The package contains parsers for file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs provides a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure and dynamics information. In addititon, 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 UI of Gromacs applications.
JGromacs is an open-source project released under the GPL (GNU General Public License). It was developed by Márton Münz and Prof Philip C Biggin at the Structural Bioinformatics and Computational Biochemistry Unit at the Department of Biochemistry in the University of Oxford.
You can access the JavaDoc documentation of JGromacs v1.0. here as a gzipped tar file. The complete JGromacs v1.0 documentation (explanations of all the subpackages, classes and methods, a Quick Start Guide and examples) can be downloaded from here.
The best way to start using JGromacs is to look at the Quick Start Guide and use the library of example codes which come complete with an example test data set.
If you use jgromacs in your work, please cite:
Jgromacs: a Java package for analyzing protein simulations.
Munz M & Biggin PC. J. Chem. Inf. Model. 2012. 255-259.
The JGromacs v1.0. package (binaries in a jar file) can be downloaded from here. You can also download JGromacs v1.0. source codes (in a gzipped tar file) from here. You can validate your installation by running the comprehesnive JUnit test suite created for the package which is available here in a gzipped tar file.
The whole JGromacs package comes as a single JAR (Java ARchive) file that can be added as an external library to the build path of a Java project. If you need further instructions for installing the API, running the example codes and the test suite, please see the installation guide (also available in the documentation).
Although this code is now legacy and not maintained, we are happy to discuss any aspect of it.