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JGromacs: A Java Package for Analyzing Protein Simulations

Márton Münz, Philip C. Biggin
2012 Journal of Chemical Information and Modeling  
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.  ...  However, GROMACS is the only package of the four that is open-source. The GROMACS suite also includes a series of tools to process and analyze trajectories generated by simulations.  ... 
doi:10.1021/ci200289s pmid:22191855 pmcid:PMC3269218 fatcat:f5mce7mqkrasvibccgrvm3rnbq