bbye98/gcme

Source code for journal article "GCMe: Efficient Implementation of the Gaussian Core Model with Smeared Electrostatic Interactions for Molecular Dynamics Simulations of Soft Matter Systems" by Benjamin Ye, Shensheng Chen, and Zhen-Gang Wang

Gaussian core model with smeared electrostatics (GCMe)

This repository contains the code used in the journal article

Ye, B. B.; Chen, S.; Wang, Z.-G. GCMe: Efficient Implementation of Gaussian Core Model with Smeared Electrostatic Interactions for Molecular Dynamics Simulations of Soft Matter Systems. 2024. https://doi.org/10.48550/ARXIV.2403.08148.

Pre-requisites

The Python scripts require

• Python 3.9 or later,
• OpenMM,
• MDCraft 1.1 or later and its dependencies, and
• either constvplugin or openmm-ic-plugin

to be installed.

The LAMMPS scripts have been tested to run on the 21 Nov 2023 release with the fix imagecharges command from lammps-fix-imagecharges. Older LAMMPS builds will likely have to use the fix imagecharges command from lammps-fixes instead due to recent internal LAMMPS API changes.

Directory

├── benchmark
│   ├── ljcoul_ic_real.lmp      # LAMMPS: WCA/Coulomb system w/ image charges
│   ├── ljcoul_slab_real.lmp    # LAMMPS: Slab WCA/Coulomb system
│   ├── ljcoul_ic.py            # OpenMM: WCA/Coulomb system w/ image charges
│   ├── gcme_bulk_real.lmp      # LAMMPS: Bulk GCMe system
│   ├── gcme_ic_real.lmp        # LAMMPS: GCMe system w/ image charges
│   ├── gcme_slab_real.lmp      # LAMMPS: Slab GCMe system
│   └── gcme_all.py             # OpenMM: GCMe systems w/ all three BCs
├── analysis_gcme.ipynb
├── npt_water.py
├── nvt_polyanion_counterion_solvent.py
└── nvt_water.py

The benchmark directory contains scripts to run simulations of simple coarse-grained systems for the benchmark results in the "Performance" section of the paper.

The npt_water.py script runs NpT simulations of coarse-grained "water" particles at different pressures and repulsion parameters to determine the key GCMe parametrization relationship in the "Parametrization" section of the paper. The nvt_water.py script runs NVT simulations of the parametrized GCM so that the most probable pair separation distance can be determined using the radial distribution function.

The nvt_polyanion_counterion_solvent.py script runs NVT simulations of polyanions, their counterions, and solvent particles confined between two planar perfectly conducting or nonmetal electrodes using OpenMM as part of the "Illustrative examples" section of the paper.

The analysis_gcme.ipynb Jupyter notebook analyzes and plots all equations and simulation data included in the paper.