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Illinois Tools: NanoGromacs

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 1.3.1 - published on 31 May 2011

doi:10.4231/D35T3G01C cite this

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Tools

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Abstract

NanoGromacs is an interface for molecular dynamic simulation using Gromacs. It can perform lipid and protein simulations on user provided structures. The users can upload their own input structures, select corresponding force field files and set the run-time parameters. The simulation result structure can be visualized using PyMOL on the nanoHUB. The interface also can show the dynamic effect of the simulation process. The simulation result also can be analyzed by utilities from Gromacs. The users can also download the result pdb file then use their favorite visualization tool like VMD or RasMol to view it locally.

NanoGromacs simplifies the task of assembling the input files required. It ignores tedious command line execution of Gromacs. And it also provides users with visualization result and analysis tools.

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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; Eric Jakobsson (2011), "Illinois Tools: NanoGromacs," http://nanohub.org/resources/nanogromacsii. (DOI: 10.4231/D35T3G01C).

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