NAMD

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

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