Programme Parameters
Advanced Postgrad
3 Days (4.5 Hrs)
Online (e-LMS)
• Prior working knowledge of the field and comfort with core tools and quantitative reasoning.
• A laptop or desktop with a stable internet connection.
• Willingness to complete assignments and the capstone project.
About This Course
Real-World Applications Apply Advanced Molecular Dynamics Simulations of Protein Structure using GROMACS skills directly to academic research, thesis work, and publications. Every participant receives a verified e-Certificate and e-Marksheet from the Deep Science & Technology Consortium.
🎯 Program Aim
Real-World Applications
Apply Advanced Molecular Dynamics Simulations of Protein Structure using GROMACS skills directly to academic research, thesis work, and publications
📋 Course Objectives
1. Apply biotechnology methods to authentic research and industry problems.
2. Produce a reproducible, portfolio-ready project you can cite in a thesis, paper, or job application.
👥 Who Should Enroll?
• Master's and senior undergraduate students specializing in biotechnology
• R&D engineers and working professionals applying biotechnology in industry
• Academics and educators building research or teaching capacity in biotechnology
🚀 Key Learning Outcomes
• A demonstrable biotechnology project for your research or industry portfolio.
• A verified e-Certificate of competency and e-Marksheet from the Deep Science & Technology Consortium.
💎 What You'll Gain
Live & Recorded Sessions
Lifetime access to class recordingse-Certificate on Completion
Cryptographically verified credentialPost-Programme Support
Direct access to mentors & councilHands-On Experience
Notebooks, real-world code & datasetsCurriculum Outline
System Preparation
• Structure preparation: missing residues, protonation states and disulphides
• Force field selection (AMBER, CHARMM, GROMOS) and the consequences of the choice
• Solvation, ion placement and box geometry to avoid periodic image artefacts
Energy Minimisation and Ensembles
• Minimisation, NVT and NPT equilibration with position restraints
• Thermostats and barostats: correct choices for production versus equilibration
• Verifying equilibration rather than assuming it from wall-clock time
Running and Scaling Simulations
• Integration timestep, constraints and hydrogen mass repartitioning
• GPU acceleration, domain decomposition and realistic performance tuning
• Checkpointing, extending runs and managing trajectory storage
Extracting Meaning From a Trajectory
• RMSD, RMSF, radius of gyration and hydrogen-bond analysis
• Principal component analysis and free energy landscapes
• Convergence assessment and why a single trajectory rarely suffices
Binding and Perturbation Methods
• MM-PBSA and MM-GBSA: usefulness and well-documented limitations
• Alchemical free energy perturbation and thermodynamic integration
• Error estimation and reporting simulation results honestly
Technical Specifications
| Parameter | Requirement |
|---|---|
| Covered Tool / Platform | RStudio |
Frequently Asked Questions
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