Simulating Water with Molecular Dynamics

This repository contains a basic simulation of water with Molecular Dynamics using GROMACS (GROningen MAchine for Chemical Simulations). This is an assignment to evaluate a Ph.D. candidate's starting skills and knowledge. A basic report is included in the report directory.

Representation of the simulation box

Environment and Python Setup

The present code was developed using the following system. It is recommended to use a similar setup to avoid any issues:

• Ubuntu 23.04
• Python 3.11.2
• GROMACS 2023.1

To replicate the Python setup, create a new environment using venv and install the packages in the requirements.txt file.

python3 -m venv venv
source env/bin/activate
pip install -r requirements.txt

Running the code

To run the main simulations, cd into the sims directory and run the corresponding files for each step.

cd sims
./init.sh   # runs the initialization of the system
./emin.sh   # runs the energy minimization run
./equi.sh   # runs the equilibration run
./prod.sh   # runs the production run

Running the benchmarks

To run the benchmarks, cd into the benchmarks directory and run the python file that automates the process.

cd benchmarks
python3 benchmarks.py

Generating the plots

To generate the plots, cd into the plots directory and run the python file for the corresponding plot. This will only work if the simulations and/or benchmarks have been previously run.

cd plots
python3 bench.py  # generates the benchmarks plot
python3 emin.py   # generates the energy minimization plot
python3 equi.py   # generates the equilibration plot
python3 rdf.py    # generates the radial distribution plot