NAMD
A parallel molecular dynamics simulation package for biomolecular systems.
Overview
NAMD is a parallel 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 http://www.ks.uiuc.edu/Research/namd/2.14/download/NAMD_2.14_Source.tar.gz tar xvf NAMD_2.14_Source.tar.gz cd NAMD_2.14_Source
- Configure and compile:
./config Linux-x86_64-g++ --charm-arch netlrts-linux-x86_64 cd Linux-x86_64-g++ make -j 4
Basic Usage
Preparing Input Files
- Prepare protein structure file (PDB format)
- Generate topology file:
psfgen -pdb protein.pdb -psf protein.psf
- Define simulation box:
solvate -psf protein.psf -pdb protein.pdb -o solvated
Energy Minimization
- Prepare energy minimization parameters
- Run energy minimization:
namd2 +p4 em.conf
Molecular Dynamics Simulation
- Prepare MD parameters
- Run MD simulation:
namd2 +p4 md.conf
Advanced Topics
Analysis Tools
- RMSD analysis
- RMSF analysis
- Secondary structure analysis
- Energy analysis
Performance Optimization
- GPU acceleration
- Parallel computing
- Memory optimization