Simulation Two Chain PAA

Summary: PLUMED-patched GROMACS molecular dynamics simulations repository used for studying the multi-valent ion mediated interactions between two polyanions.
Authors: Alec Glisman, Sriteja Mantha
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Project structure

Each subdirectory contains its own README.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.
• CITATIONS.md: List of citations for the project.
• LICENSE: Project license file.

The molecular dynamics simulations are contained in the following subdirectories:

• data: Data files output from simulation.
• force-fields: Force fields in GROMACS format used to model various system components.
• initial-structure: Energy minimized initial structures for polyelectrolytes and crystalline lattices.
• parameters: GROMACS mdp parameter files and simulation pipeline input variables.
• 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.

Configuration

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

Software and environment

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

• Bash 5.1.16
• CMake 3.22.1
• CUDA 11.8
• GCC 10.4.0
• Gromacs 2022.3 (Plumed patched and user patched share/top/residuetypes.dat)
• Plumed 2.8.1
• Packmol 20.010
• Python 3.10.6

Nomenclature

Chemistry

• Acr: Acrylic acid
• P: Poly, as in polymer
• mer: Monomer

Numerical

• EM: Energy minimization

Statistical mechanics

• NVE: Microcanonical ensemble
• NVT: Canonical ensemble
• NPT: Isothermal–isobaric ensemble