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.

Gromacs

Biophysics & Computational Biology Group

University of Illinois at Urbana-Champaign

If you reference this work in a publication, please cite as follows:

• Chen, Dairui; Kearney, Derrick; Mashl, Jay; Sobh, Nahil; Jakobsson, Eric (2008), "NanoGromacs," doi: 10254/nanohub-r4123.3.

  BibTex | EndNote

In addition, we would appreciate it if you would add the following acknowledgment to your publication:

• Simulation services for results presented here were provided by the Network for Computational Nanotechnology (NCN) at nanoHUB.org

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