KG_PGNs: Polymer Grafted Nanoparticle (PGN) Coarse-Grained Mechanical Models

Overview

Welcome to KG_PGNs, a comprehensive toolkit designed to build and simulate coarse-grained mechanical models of Polymer Grafted Nanoparticles (PGNs). This repository is based on the published work:

Moussavi, Arman, et al. "Characterizing the shear response of polymer-grafted nanoparticles." The Journal of Chemical Physics, 160.13 (2024).

The workflow includes generating initial configurations, setting up and running simulations, and analyzing results.

Getting Started

DEPOT

All necessary files originate from the DEPOT. Follow these steps to utilize the DEPOT:

1. Copy and Rename the Directory: Copy the DEPOT directory and rename it to match your system of interest. For example:

   PGN_R1_rho05_N20

2. Configure PGN Parameters: Inside the new directory, open create_PGNs.py and enter the parameter space of interest in the section labeled "PGN Parameters".

   chain_length = 20
   num_grafts = 60  # to match the grafted density
   NP_radius = 5
   gd = '05'

   Executing create_PGNs.py will build an initial configuration of 32 PGNs arranged in a face-centered cubic (FCC) lattice and write the data to a LAMMPS data file. Additionally, it will output a text file with the PGN IDs needed for the simulation input files.

3. Setup Initial Configuration: In the new directory, update the in_nvt.inp file:

   • Change the read_data field to match your system.
   • Update the group pgn id fields according to the system of interest.

4. Modify Input Scripts: In the input_scripts directory, update change_mole_bond_swap.py with the parameters of interest and execute the code to ensure the data file format is correct for usage.

5. Update INP Files: Manually update each INP file within input_scripts, using the PGN IDs from the create_PGNs.py output text file to ensure correct nanoparticle identification throughout all simulations.

6. Run Simulations: In the main renamed directory, open KG_PGN.py, enter the correct simulation details at the beginning of the file, and execute the code to submit all jobs (simulations) specified in KG_PGN.py. For more details on the methods used, refer to AutoMD.py.

   simulation_details = {
       "temperature": 300,
       "pressure": 1.0,
       "duration": 1000000
   }

   Assuming all specifications and modifications are correctly implemented, simulation output files should be generated with ease.

Analysis

Within the ANALYSIS directory, you will find various scripts to analyze the simulation results. While these scripts are designed for specific workflows, they can be modified or extended to suit your analysis needs. For specific questions, please contact the author.

Feel free to reach out for further clarification or assistance with the workflow and analysis.

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