Molecular Dynamics & Simulations

Molecular dynamics simulation tools for studying the physical movements of atoms and molecules. Investigate protein dynamics, drug interactions, and material properties at the atomic scale.

Overview

This collection includes workflows for:

• Biomolecular Simulations - Protein and nucleic acid dynamics
• Materials Science - Classical MD for materials and polymers
• Free Energy Calculations - Binding affinity and thermodynamics
• Enhanced Sampling - Metadynamics and replica exchange methods
• Trajectory Analysis - Post-simulation analysis and visualization

Available Workflows

Browse the workflows in this category to find molecular simulation tools. Each workflow includes setup guides, force field options, and analysis utilities.

System Requirements

CPU-Only:

• CPU: 16+ cores
• RAM: 32GB minimum
• Storage: 500GB+ SSD

GPU-Accelerated (Recommended):

• CPU: 8-16 cores
• GPU: NVIDIA RTX 3090, A100, or better
• RAM: 64GB+
• Storage: 1TB+ NVMe SSD

Getting Started

Deploy molecular dynamics workflows:

# Deploy an MD simulation
dxflow compose create --identity <workflow-name> <compose-file>
dxflow compose start <workflow-name>

Explore the workflows below to start your molecular simulations!