LAMMPS
A versatile molecular dynamics simulation package for biomolecular systems.
Overview
LAMMPS is a molecular dynamics simulation package designed for high-performance simulation of large biomolecular systems. It is widely used in computational chemistry and biophysics.
Features
- High-performance molecular dynamics simulations
- Energy minimization
- Free energy calculations
- Extensive analysis tools
- GPU acceleration support
Installation
Requirements
- C++ compiler (GCC 7.0+)
- CMake 3.10+
- MPI library (optional)
- CUDA toolkit (for GPU support)
Installation Steps
- Download the source code:
wget https://github.com/lammps/lammps/archive/refs/tags/stable_29Oct2020.tar.gz tar xvf stable_29Oct2020.tar.gz cd lammps-stable_29Oct2020
- Configure and compile:
mkdir build cd build cmake .. make -j 4
Basic Usage
Preparing Input Files
- Prepare protein structure file (PDB format)
- Generate topology file:
lmp -in in.protein
- Define simulation box:
lmp -in in.solvate
Energy Minimization
- Prepare energy minimization parameters
- Run energy minimization:
lmp -in in.em
Molecular Dynamics Simulation
- Prepare MD parameters
- Run MD simulation:
lmp -in in.md
Advanced Topics
Analysis Tools
- RMSD analysis
- RMSF analysis
- Secondary structure analysis
- Energy analysis
Performance Optimization
- GPU acceleration
- Parallel computing
- Memory optimization