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Illinois Tools: NanoGromacsDemo

By Dairui Chen1, Derrick Kearney2, Jay Mashl1, Nahil Sobh1, Eric Jakobsson1

1. University of Illinois at Urbana-Champaign 2. Purdue University

Implementation of the popular molecular dynamics software suite GROMACS

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Version 2.1.2 - published on 26 Aug 2014

doi:10.4231/D3599Z272 cite this

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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.

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Biophysics & Computational Biology Group

University of Illinois at Urbana-Champaign

Cite this work

Researchers should cite this work as follows:

  • Dairui Chen; Derrick Kearney; Jay Mashl; Nahil Sobh; Eric Jakobsson (2014), "Illinois Tools: NanoGromacsDemo," (DOI: 10.4231/D3599Z272).

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Tags, a resource for nanoscience and nanotechnology, is supported by the National Science Foundation and other funding agencies. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.