NanoGromacs is an interface for performing molecular dynamics (MD) simulations using Gromacs. Users can perform protein simulations by uploading their own structure file or running the 4 examples provided, 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.

Gromacs

Biophysics & Computational Biology Group

University of Illinois at Urbana-Champaign

Researchers should cite this work as follows:

• Dairui Chen; Jay Mashl; Nahil Sobh; Eric Jakobsson (2011), "Illinois Tools: NanoGromacs_Intro," https://nanohub.org/resources/nanogromacsdemo. (DOI: 10.4231/D39K45S6K).

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1. nanobio applications
2. NCN@Illinois Supported
3. NCN Supported