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3.4

25 votes

Bruce Allen

I saw NanoEngineer-1 as an opportunity to build a poor man's suit. I modified its python code to use atom types for the published COMPASS force field. The user simply builds molecules and adds atom types to the model. The Molecular Machine Part file now contains the atom types for a specific force field. This file format is native to the NanoEngineer-1 software.

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.

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