NanoEngineer-1
Open-source 3D multi-scale modeling and simulation program for nano-composites
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NanoEngineer-1 is an open-source (GPL) 3D multi-scale modeling and simulation program for nano-composites with special support for structural DNA nanotechnology. It features an easy-to-use interactive 3D graphical user interface for designing and modeling large, atomically precise composite systems.
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One can now feed NanoEngineer-1 files to PACKMOL to build large systems of molecules. The atom types are passed to the PACKMOL output file.
Finally, the PACKMOL output file is passed to msi2lmp software to generate the LAMMPS input file. This final file contains atom types and potentials for them. LAMMPS makes use of the data in the simulation.
The NanoEngineer-1 software could be modernized by doing ring detection, auto-typing atoms, support many force fields, call LAMMPS molecular mechanics energy minimizers , and other changes. The software is brittle due to Python. It needs to be refreshed from 2.7 to 3.11 at a minimum. Ideally, The software should be rewritten using a serious language e.g C++ so it can be maintained.