LAMMPS

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

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