Title: Molecular Dynamics Certification Course - 18 Hours

Module 1: Introduction to Molecular Dynamics (2 hours)

• Understanding Molecular Dynamics Simulation
• Applications in Biophysics, Chemistry, and Material Science
• Overview of Software and Tools

Module 2: Basics of Molecular Modeling (3 hours)

• Molecular Structures and Force Fields
• Energy Minimization Techniques
• Initial Setup for Molecular Dynamics Simulations

Module 3: Simulation Protocols (2 hours)

• Ensemble Types: NVE, NVT, NPT
• Integration Algorithms: Verlet, Leapfrog
• Temperature and Pressure Control Methods

Module 4: Advanced Techniques (4 hours)

• Free Energy Calculations
• Enhanced Sampling Methods
• Replica Exchange Molecular Dynamics (REMD)

Module 5: Analysis and Visualization (3 hours)

• Trajectory Analysis: RMSD, RMSF, Dihedral Angles
• Visualization Tools: VMD, PyMOL
• Interpretation of Simulation Results

Module 6: Applications in Biophysics and Drug Discovery (2 hours)

• Protein-Ligand Interactions
• Understanding Enzyme Mechanisms
• Drug Binding and Design

Module 7: Case Studies and Practical Sessions (2 hours)

• Real-world Applications
• Hands-on Practice with Molecular Dynamics Software
• Troubleshooting and Best Practices

Module 8: Certification Exam Preparation (2 hours)

• Review of Key Concepts
• Practice Questions and Problem Solving
• Exam Guidelines and Tips

Certification Exam (1 hour)

• Comprehensive Exam Covering Course Material
• Practical Application Assessment
• Certification Awarded Upon Successful Completion

This 18-hour Molecular Dynamics Certification Course is designed to provide a thorough understanding of molecular dynamics simulations, from fundamental principles to advanced applications. Participants will gain hands-on experience, practical insights, and the skills needed to apply molecular dynamics in various scientific domains.