Updated README.md with getting started instructions

README.md

@@ -2,10 +2,54 @@
 
 A molecular dynamics code for a Lennard-Jones system.
 
-The purpose is to provide a basic molecular dynamics code base (`CHEG231MD.py`) written in fairly plain Python and standard libraries. The code is used as part of a module on molecular thermodyanmics in the University of Delaware Chemical Engineering Thermodynamics I course's honors section. Students use it explore the basic concepts of molecular simulations and molecular processes in thermodynamics. 
+The purpose is to provide a basic molecular dynamics code base (`CHEG231MD.py`) written in fairly plain Python and standard libraries. The code is used as part of a module on molecular thermodynamics in the University of Delaware Chemical Engineering Thermodynamics I course's honors section. Students use it to explore the basic concepts of molecular simulations and molecular processes in thermodynamics.
 
 *SimpleMD* is not a high performance simulation. Those seeking modern simulation tools should use LAMMPS or other powerful packages.
 
-See the accompanying manual, *Really Simple Molecular Dyanmics with Python* for instructions on getting started and exercises to try with the code. `MDsim.ipynb` is a Jupyter notebook used in the second section of the text.
+See the accompanying manual, *Really Simple Molecular Dynamics with Python*, for instructions on getting started and exercises to try with the code.
 
-Also included here is a Jupyter notebook for calculating the Maxwell-Boltzmann distribution. Students can use simulation results to compare with the distribution.
+## Getting started
+
+### 1. Clone the repository
+
+```bash
+git clone https://lem.che.udel.edu/git/furst/SimpleMD.git
+cd SimpleMD
+```
+
+### 2. Create a Python virtual environment
+
+Create and activate a virtual environment using Python's built-in `venv` module:
+
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+```
+
+On Windows, activate with:
+```
+.venv\Scripts\activate
+```
+
+### 3. Install dependencies
+
+```bash
+pip install numpy numba matplotlib jupyter
+```
+
+### 4. Run the simulation
+
+Launch Jupyter and open `MDsim.ipynb`:
+
+```bash
+jupyter notebook MDsim.ipynb
+```
+
+The notebook walks through creating a simulation, running it, and analyzing the results. See the manual for detailed instructions and exercises.
+
+## Contents
+
+- `CHEG231MD.py` — the molecular dynamics simulation code
+- `MDsim.ipynb` — Jupyter notebook for running and analyzing simulations
+- `maxwell boltzmann/` — Jupyter notebook for calculating the Maxwell-Boltzmann distribution; students can compare simulation results with the distribution
+- `SimpleMD_manual.pdf` — the manual, *Really Simple Molecular Dynamics with Python*