Schrödinger: Molecular Dynamics Simulation (MDS)

Description

💻 3-Day Hands-On Workshop | 🕒 1–1.5 Hours/Day

Day 1: Introduction & System Preparation

• Overview of Schrödinger Suite & Desmond
• Installing & launching Maestro (GUI intro)
• Protein Preparation Wizard:
  • Importing structure (PDB)
  • Preprocessing, assigning bond orders, adding hydrogens
  • Removing waters, fixing missing residues
• Ligand preparation (LigPrep basics)
• Building the system: Solvation, box type, ions, force fields
• Practice: Prepare a protein-ligand complex for simulation

Day 2: Running Molecular Dynamics in Desmond

• MD workflow: Minimization → Relaxation → Production run
• Setting up simulation parameters: time, temperature, ensemble
• Using default .cfg or customizing simulation settings
• Submitting jobs on local or remote host (CPU/GPU)
• Monitoring MD progress in Maestro
• Output files: .cms, .dtr, .trj, .ene, .log
• Practice: Launch and monitor a short MD simulation

Day 3: Trajectory Analysis & Interpretation

• Analyzing trajectories using Simulation Event Analysis & Simulation Interactions Diagram
• Key metrics:
  • RMSD, RMSF
  • Radius of Gyration (Rg)
  • H-Bonds, SASA, contacts
  • Interaction timeline & ligand stability
• Visualization tips: rendering, coloring, snapshot export
• Exporting graphs and summary reports
• Q&A and guidance on real-world research projects