School of Bioinformatics · Structural biology & drug discovery
Molecular Dynamics Simulations with GROMACS
Molecular dynamics shows how proteins and their complexes move. This course teaches how to set up, run and analyse simulations with GROMACS, and how to tell a meaningful result from an artefact of a short or poorly prepared run.
Course overview
Molecular Dynamics Simulations covers the physics you need (force fields, integrators, thermostats, periodic boundaries) and the practical workflow: preparing a protein, solvating it, minimising, equilibrating and running production simulations.
You simulate a protein and a protein–ligand complex, analyse stability, flexibility, hydrogen bonds and interaction persistence, estimate binding energies with MM/PBSA while understanding its limits, and learn the reporting standards that reviewers increasingly expect.
Learning outcomes
By the end of the course you will be able to:
- Explain force fields, ensembles and the main simulation parameters
- Prepare, solvate, minimise and equilibrate a system in GROMACS
- Parameterise a ligand and simulate a protein–ligand complex
- Analyse RMSD, RMSF, hydrogen bonds, contacts and clusters
- Estimate binding free energy with MM/PBSA and report simulations reproducibly
Skills you will practise
Eligibility and prerequisites
Who can apply
- Students and graduates of B.Sc., M.Sc., B.Tech., M.Tech., B.Pharm., M.Pharm., MBBS, BDS, B.V.Sc. or a PhD programme in the life sciences, biotechnology, bioinformatics, pharmacy, medicine, agriculture, chemistry, statistics or computer science
- Researchers, faculty and industry professionals moving into data-driven biology
- Final-year students may apply before their results are declared
Prerequisites
- Linux command line
- Molecular Docking or Protein Structure course, or equivalent
Best suited to
- Researchers validating docking results
- Structural biologists and biophysicists
- Pharmacy and chemistry postgraduates in drug discovery
Module-wise syllabus
6 modules. Each pairs instructor-led sessions with a hands-on lab on public data.
Topics
- Force fields and potential energy
- Integrators, thermostats and barostats
- Periodic boundaries and electrostatics
Topics
- Cleaning structures and protonation states
- Solvation and ions
- Minimisation and equilibration
Topics
- Production runs and sampling
- RMSD, RMSF and radius of gyration
- Clustering and PCA
Topics
- Ligand topologies with CGenFF or ACPYPE
- Restraints and equilibration
- Interaction persistence
Topics
- MM/PBSA and its limits
- Replicates and convergence
- Reporting checklists
Topics
- Simulation design
- Analysis
- Report
Practical sessions and projects
Capstone project
Test a docked pose with MD
Run replicate simulations of a protein–ligand complex, analyse its stability and interactions, and report whether the docking hypothesis survives, with uncertainty.
Assessed on the correctness of the analysis, the quality of the code and the reasoning in the write-up. A pass is required for the certificate.
- Physics for simulators
Run a short simulation of a small system and see how the time step and thermostat change the result.
- Preparing a system
Prepare and equilibrate lysozyme in water and check temperature, pressure and density.
- Production and analysis
Analyse a protein trajectory and identify flexible regions and dominant motions.
- Protein–ligand simulations
Simulate a docked complex and measure which contacts persist over the trajectory.
- Binding energies and good practice
Estimate MM/PBSA energies across replicate runs and quantify their uncertainty.
- Project: validate a docking pose
Use replicate simulations to test whether a docked pose is stable and write up the result with its caveats.
Software, tools and datasets
Software and tools
All software is free and open source or free for academic use. Recommended computer: 8 GB RAM, 30 GB free disk, Linux, macOS or Windows with WSL2.
Datasets
- Hen egg-white lysozyme: System preparation tutorial.RCSB PDB 1AKI
- HIV-1 protease–inhibitor complex: Protein–ligand simulation.RCSB PDB 1HSG
Core reading
- Abraham MJ et al. (2015). GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2:19–25.
- Lemkul JA (2019). From proteins to perturbed Hamiltonians: a suite of tutorials for the GROMACS-2018 molecular simulation package. Living Journal of Computational Molecular Science 1:5068.
Duration, format and fees
- Next cohort
- Dates are sent with your admission offer
- Timetable
- Three evening or weekend sessions a week (IST), plus a lab clinic; intensive and weekend-only schedules on request
- Payment
- Secure online payment link with your admission offer (UPI, cards, net banking). Instalments on request for fees above ₹15,000.
- Refunds
- See the refund and cancellation policy.
Instructor
The instructor for each cohort is named in your admission offer and on this page when the cohort is announced. Vedicgen instructors are selected for hands-on research or industry experience in the subject they teach, and every course is reviewed by a second subject expert.
Questions about who teaches a cohort? [email protected]
Certificate
Learners who complete the course and pass its capstone receive a Vedicgen certificate of completion for Molecular Dynamics Simulations with GROMACS, issued by Vivofold, stating the guided hours and skills assessed. Each certificate has a unique ID and QR code that anyone can check.
Apply for Molecular Dynamics Simulations with GROMACS
Apply
Send the form below. It takes about five minutes.
Review
An adviser confirms your fit and format within two working days.
Offer
You receive dates, timetable and a secure payment link.
Onboard
Set-up guide, pre-reading and joining links.
Frequently asked questions
No. Lab clinics provide access to the course server for production runs. A laptop is enough for preparation and analysis.
In the live cohort, modules are taught in instructor-led sessions with a weekly lab clinic where you work on real public data with help at hand; every session is recorded. The self-paced format uses the same lessons, labs and datasets with mentor review of your capstone. Both formats end with an assessed project reviewed for the code and the science.
A laptop with at least 8 GB of RAM and about 30 GB of free disk space, running Linux, macOS, or Windows with WSL2. Installation instructions are sent before the first session, and lab clinics help with any set-up problems.
Yes. Learners who complete the course and pass its assessment receive a Vedicgen certificate of completion, issued by Vivofold. Every certificate carries a unique ID and a QR code that anyone, including an employer or admissions office, can check on the certificate verification page.
Apply with the form on this page. Live and in-person cohorts run through the year; the dates, timetable and joining details of the next cohort are sent with your admission offer and listed on this page once announced. Self-paced enrolment opens as soon as your application is accepted.
Yes. No course runs longer than four weeks, and the length is customisable: choose the standard schedule, an intensive one- to two-week schedule, weekends only, or a custom timetable. Pick your preference on the application form; colleges and teams can book their own dates.
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