Desmond
A high-performance molecular dynamics simulation package for biomolecular systems.
Overview
Desmond is a high-performance molecular dynamics simulation package developed by D.E. Shaw Research. It is designed for simulating biomolecular systems with exceptional performance and accuracy.
Features
- GPU-accelerated molecular dynamics
- Advanced sampling methods
- Free energy calculations
- Enhanced sampling techniques
- High-performance parallel computing
- Comprehensive analysis tools
- Integration with Maestro GUI
Installation
Requirements
- Linux/Unix operating system
- NVIDIA GPU with CUDA support
- CUDA toolkit 11.0+
- 16GB+ RAM
- 50GB+ disk space
Installation Steps
- Download Desmond:
wget https://www.deshawresearch.com/downloads/download_desmond.sh chmod +x download_desmond.sh ./download_desmond.sh - Install dependencies:
sudo apt-get update sudo apt-get install cuda-toolkit-11-0
Basic Usage
Example Configuration
# Desmond 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
Desmond 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