ACEMD
A high-performance GPU-accelerated molecular dynamics simulation package.
Overview
ACEMD is a GPU-accelerated molecular dynamics simulation package developed by Acellera. It is designed for high-performance simulations of biomolecular systems, offering exceptional speed and accuracy.
Features
- GPU-accelerated molecular dynamics
- Support for multiple force fields
- Enhanced sampling methods
- Free energy calculations
- High-performance parallel computing
- Comprehensive analysis tools
- Integration with HTMD
Installation
Requirements
- Linux/Unix operating system
- NVIDIA GPU with CUDA support
- CUDA toolkit 11.0+
- 16GB+ RAM
- 50GB+ disk space
Installation Steps
- Download ACEMD:
wget https://www.acellera.com/downloads/acemd.tar.gz tar xzf acemd.tar.gz - Install dependencies:
sudo apt-get update sudo apt-get install cuda-toolkit-11-0
Basic Usage
Example Configuration
# ACEMD configuration file
set type = MD
set ensemble = NPT
set temperature = 300
set pressure = 1.01325
set timestep = 2.0
set cutoff = 9.0
set nsteps = 10000
set nstxout = 1000
set nstvout = 1000
set nstfout = 1000
set nstlog = 1000Advanced Topics
Enhanced Sampling
ACEMD supports various enhanced sampling methods:
- Replica Exchange Molecular Dynamics (REMD)
- Metadynamics
- Accelerated Molecular Dynamics (aMD)
- Temperature Replica Exchange
Performance Optimization
- GPU acceleration
- Parallel computing
- Memory optimization
- Load balancing