Lennard-Jones Gas Molecular Dynamics Simulation

This project performs a molecular dynamics simulation of a simple gas using the Lennard-Jones (LJ) potential to model interactions between particles. The simulation uses the Velocity Verlet integrator and supports trajectory output in the PDB format for visualization.

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About This Project

This project was developed as a learning exercise in molecular dynamics and C/Fortran programming. It simulates a simple gas using the Lennard-Jones potential and implements key MD features such as force calculation, integration, and trajectory output. While it’s not production-ready, it serves as a solid foundation for understanding and extending MD techniques.

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Features

• Simulation of 3D particles interacting via Lennard-Jones potential
• Periodic boundary conditions with minimum image convention
• Velocity initialization using Maxwell-Boltzmann distribution (Fortran subroutine)
• Velocity Verlet integration
• Output trajectory in PDB format
• Customizable parameters via md.mdp configuration file
• Progress bar display

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File Structure

• main.c – Entry point for the simulation.
• md.c – Implements the core MD algorithm: force computation and integration.
• utils.c – Handles file I/O (PDB and MDP files), progress bar, and utility functions.
• init_velocities.f90 – Fortran routine to initialize particle velocities.
• atom.h, params.h, constants.h – Definitions for atoms, parameters, and constants (not provided here but assumed to be included).

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How to Build

You need a C compiler and a Fortran compiler (e.g., gcc and gfortran):

gfortran -c init_velocities.f90 -o init_velocities.o
gcc -c utils.c md.c main.c
gcc main.o md.o utils.o init_velocities.o -o md_sim -lgfortran -lm

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How to Run

./md_sim

Make sure the following files are in the same directory:

• h.pdb – Initial atomic coordinates (PDB format).
• md.mdp – Simulation parameters.

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md.mdp Parameters

Example contents:

dt = 0.005
nsteps = 1000
ref_temp = 300.0
ref_press = 1.0
rcut = 2.5
skip = 100

• dt – Timestep (in reduced units)
• nsteps – Total simulation steps
• ref_temp – Reference temperature for velocity initialization
• ref_press – Placeholder (not used currently)
• rcut – Cutoff radius for the LJ potential
• skip – Trajectory output frequency

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Output

• testtraj.pdb – Appends a PDB frame every skip steps. Can be viewed in molecular viewers like VMD, PyMOL, or Chimera.

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Known Limitations

• No thermostat or barostat is implemented
• Only supports Lennard-Jones interactions
• No parallelization or performance optimization
• Assumes all atoms have the same mass

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License

This project is released under the MIT License. Feel free to modify and use it for educational or research purposes.