BIO HELP LEARNING COURSE

Molecular Dynamics Simulation with GROMACS

Run and analyse protein and protein–ligand molecular dynamics with GROMACS: system setup, force fields, equilibration, production runs, RMSD, RMSF and binding stability.

Drug Discovery

◉ Advanced◷ 15 Hours▣ Certificate Included

Course Information

Everything you need to know before enrolling.

LANGUAGEEnglish

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Registration for the next live batch opens soon. Pre-register and our team will contact you with the batch dates, fees and registration link as soon as it opens.

Live online classes
Group & college batches
Certificate on completion

Pre-register for live training → Ask on WhatsApp Or email [email protected]

▤ Overview ☷ Curriculum ♙ Instructor ☆ Reviews ▣ FAQs

▤

About This Course

Docking gives a snapshot; molecular dynamics shows how a complex moves and whether a ligand stays bound. This course teaches the complete GROMACS workflow used in structural biology and drug discovery research.

You prepare proteins and ligands, choose force fields, solvate and neutralize systems, run energy minimization and equilibration, perform production simulations, and analyse stability, flexibility, hydrogen bonds and binding energies.

Who this course is for

Researchers in structural biology and drug discovery
Students who have done docking and want to validate results
Pharmacy and chemistry learners moving into computational methods

Prerequisites

AI and Cheminformatics in Drug Discovery or basic molecular docking, plus Linux command-line basics.

Final project

Simulate a protein–ligand complex and report its stability with RMSD, RMSF, hydrogen-bond and binding-energy analysis.

◎

What You’ll Learn

✓Explain the principles of molecular dynamics

✓Prepare protein and ligand topologies

✓Solvate, neutralize and minimize a system

✓Run NVT and NPT equilibration

✓Run and monitor production simulations

✓Analyse RMSD, RMSF, radius of gyration and hydrogen bonds

✓Estimate binding energies with MM-PBSA

⌘

Tools & Technologies

GROMACSCHARMM-GUIACPYPEAmberToolsPyMOLVMDgmx_MMPBSAGrace / MatplotlibLinux

Course Curriculum

What you will learn, module by module

10 modules 15 hours of training 40 topics Certificate on completion

- Why simulate molecules
- Newton's equations and integration
- Force fields explained
- Time scales and limitations
- Installing GROMACS on Linux or WSL
- The GROMACS workflow and file types
- Preparing a PDB structure
- Fixing missing atoms and residues
- Choosing a force field
- Generating topologies with pdb2gmx
- Water models
- Checking the topology
- Why ligands need parameters
- Using CHARMM-GUI or ACPYPE
- Merging protein and ligand topologies
- Common ligand errors
- Defining the simulation box
- Adding water and ions
- Energy minimization
- Checking convergence
- Temperature coupling
- Pressure coupling
- Position restraints
- Checking equilibration plots
- Setting simulation parameters
- Running on CPU and GPU
- Restarting and extending runs
- Managing trajectory files
- RMSD and RMSF
- Radius of gyration
- Hydrogen bonds and contacts
- Visualizing trajectories in VMD and PyMOL
- MM-PBSA concepts
- Running gmx_MMPBSA
- Per-residue energy decomposition
- Interpreting binding energies
- Simulate a protein–ligand complex
- Analyse stability and interactions
- Write the results report
- Presentation and feedback

♙

Your Instructor

Bio Help Learning Educator

Bioinformatics Educator & Mentor

Learn from experienced educators and practitioners through practical, career-focused bioinformatics training.

Frequently Asked Questions

6 answers about this course

Do I need a GPU?

No, but it helps. Course systems are sized to run on a normal laptop, and we show how to use GPUs and clusters for longer runs.

Do I need docking experience?

It helps to understand protein–ligand complexes. Our AI and Cheminformatics course covers docking.

Which operating system do I need?

Linux, or Windows with WSL. Setup is covered in the course.

Will I get a certificate?

Yes, after completing all modules, the quizzes and the final project.

How do I get fee and batch details?

Pre-register on this page or contact us on WhatsApp, and our team will share the details.

How long will I have access to the course?

You get full access to all course materials for 3 months from the date of enrollment.

Still have a question?Our team usually replies within one working day.

Ask on WhatsApp →

WHAT OUR LEARNERS SAY

Real Stories. Real Growth.

Hear from learners building practical skills with Bio Help Learning.

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I really enjoyed the course and found it very useful: it gave a clear and practical overview of the whole WGS workflow, from raw reads to a VCF, and the hands-on sessions helped a lot.

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The workshop provided me an understanding of the principles and techniques involved in bioinformatics, molecular docking, protein-ligand interactions, homology modeling, and drug design.

Ridam BhowmickMaulana Abul Kalam Azad University of Technology, West Bengal.Molecular Docking and Drug Discovery

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As i am from biotechnology background this workshop, actually very helpfull for me

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Learn about different molecular docking tools.

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This workshop helped me to learn working with various softwares and also to develop an interest over drug designing

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From this workshop I learned many new things such as docking, about new websites,how to use Swiss software,basic bioinformatics etc, it's very helpful for me.

Sayan DuttaUniversity of CalcuttaBioinformatics Training

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The workshop was informative and provided valuable insights into bioinformatics tools and techniques.

Santhosh M EReva University BangaloreBioinformatics Tools and Techniques

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The Drug Discovery Workshop was highly informative and helped me gain valuable knowledge about the drug discovery process, including molecular docking, drug–target interactions, and computational tools used in drug design.

ANUSHA P VCSIR-CCMB, Hyderabad IndiaDrug Discovery Workshop

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OUR GLOBAL LEARNERS