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Summary: PLUMED-patched GROMACS molecular dynamics simulations repository used for my anti-scaling research project in the Wang Group.
Authors:Alec Glisman
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Each subdirectory contains its ownREADME.md file with more detailed information about the project.We present a brief summary of each subdirectory below, but strongly recommend that users read the other documentation for a better idea of how to use the code.

The project contains many configuration and styling files for various tools, including:

• .github/: GitHub workflows and issue templates directory.
• .vscode/: Visual Studio Code editor settings and configuration directory.
• .clang-format: Clang-format configuration file for C++ code.
• .pylintrc: Pylint configuration file for Python code.
• .shellcheckrc: ShellCheck configuration file for shell scripts.
• .wakatime-project: Wakatime configuration file for time tracking.
• LICENSE: Project license file.

The molecular dynamics simulations are contained in the following subdirectories:

• data: Data files output from simulation.
• force-field: Force fields in GROMACS format used to model various system components.
• initial-structure: Energy minimized initial structures for polyelectrolytes and crystalline lattices.
• parameters: GROMACS and PLUMED input files used to run simulations.
• python: Helper Python scripts called by the simulation pipeline.
• scripts: Bash scripts used to run simulations and analyze data output using GROMACS and PLUMED command line interface tools.
• software: GROMACS and PLUMED source code and build scripts as well as environment configuration files.
• submission: Slurm job submission scripts used to run simulations on the group's HPC cluster.

Various formatting files are included (.clang-format,.pylintrc, and.shelcheckrc) to ensure consistent code formatting and style.

Further information on exact software versions can be found in thesoftware directory'sREADME.md file.We run our simulations using

• CUDA 12.2
• GCC 12.3.0
• CMake 3.22.1
• Bash 5.1.16
• Python 3.11.4
• Packmol 20.010
• Gromacs 2023.2 (Plumed patched and user patchedshare/top/residuetypes.dat)
• Plumed 2.9.0

• Asp: Aspartic acid
• Glu: Glutamic acid
• Acr: Acrylic acid
• P: Poly, as in polymer
• mer: Monomer

• EM: Energy minimization
• NVE: Microcanonical ensemble
• NVT: Canonical ensemble
• NPT: Isothermal–isobaric ensemble