NanoGromacsForBilayerProteinStructure

By Dairui Chen; Derrick Kearney; Jay Mashl; Nahil Sobh; desmond soo chin yoong

Implementation of the popular molecular dynamics software suite GROMACS

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Archive Version 2.0
Published on 08 Sep 2008, unpublished on 09 Sep 2008 All versions

doi:10.4231/D38K74W3W cite this

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Abstract

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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Gromacs

Credits

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, desmond soo chin yoong (2016), "NanoGromacsForBilayerProteinStructure," https://nanohub.org/resources/nanogromacs. (DOI: 10.4231/D38K74W3W).

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Tags

  1. educational tool
  2. Illinois
  3. nano/bio
  4. nanobio applications