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remove references to lamps
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Ragzouken committed Oct 10, 2024
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Expand Up @@ -81,7 +81,6 @@ page in our documentation for detailed instructions on installing NanoVer.
* Activate the conda environment: `conda activate nanover-dev`
* Install the required conda packages: `conda install -c conda-forge openmm MDAnalysis MDAnalysisTests ase`
* Compile the protocol and install the NanoVer libraries in your conda environment: `./win_compile.ps1`. If you do not plan on modifying the python packages, run `./win_compile.ps1 -noedit` instead. Otherwise, by default, the nanover packages will be installed in edit mode (`pip install -e`) meaning that changes in the `nanover-protocol` directory will be directly reflected in your python environment.
* The `nanover-lammps` module and its tests require MPI to be installed. Download and install Microsoft MPI from https://docs.microsoft.com/en-us/message-passing-interface/microsoft-mpi

### Mac and Linux

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* [gRPC](https://grpc.io/) (Apache v2) - Communication protocol.
* [ASE](https://wiki.fysik.dtu.dk/ase/) (LGPLv3): Atomic simulation environment used for running simulations ([citation](https://iopscience.iop.org/article/10.1088/1361-648X/aa680e)).
* [OpenMM](http://openmm.org/) (MIT, LGPLv3): GPU accelerated molecular mechanics library ([citation](https://simtk.org/plugins/publications/index.php/?group_id=161)).
* [LAMMPS](https://lammps.sandia.gov/) (GPLv2): Molecular mechanics library ([citation](https://lammps.sandia.gov/cite.html)).
* [MDAnalysis](https://www.mdanalysis.org/) (GPLv2): Molecular dynamics analysis library ([citations](https://www.mdanalysis.org/pages/citations/)).
* [NGLView](https://nglviewer.org/#nglview) (MIT): IPython/Jupyter widget to interactively view structures and trajectories ([citations](http://nglviewer.org/nglview/latest/#cite)).
* [python-osc](https://pypi.org/project/python-osc/) (Public domain) - Open sound control library.
* [MPI4Py](https://mpi4py.readthedocs.io/en/stable/index.html) ([BSD 2-clause license](https://bitbucket.org/mpi4py/mpi4py/src/master/LICENSE.rst)): MPI library for python, used with LAMMPS ([citation](https://mpi4py.readthedocs.io/en/stable/citing.html)).
* [Numpy](https://numpy.org/) (BSD) - Numerical computation library.
* [Netifaces](https://pypi.org/project/netifaces/) (MIT) - Portable library for accessing network interface information.
* [Pytest](https://docs.pytest.org/en/latest/) (MIT) - Python testing framework
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