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NanoGromacs is an interface for performing molecular dynamics (MD) simulations using Gromacs. NanoGromacs simplifies the task of assembling the input files required. Users can perform lipid and protein simulations by uploading their own structure file, selecting a corresponding force field, and setting the run-time parameters. Snapshots of coordinates generated by the simulation can be visualized on the nanoHUB, and corresponding structure files can be downloaded and visualized locally, for example, with PyMOL. Several of the analysis programs from Gromacs are also provided.
Biophysics & Computational Biology Group
University of Illinois at Urbana-Champaign