Training Program on
Date
08 - 19 Sept 2025
Time
07.30 pm IST
About the Workshop
This two-week online hands-on training on GROMACS is designed to provide participants with comprehensive knowledge and practical experience in molecular dynamics (MD) simulations. The workshop covers a wide range of topics—from fundamental concepts of MD and high-performance computing (HPC) to advanced simulations involving protein-ligand, membrane-protein, metal complexes, and nanomaterial interactions. Participants will gain hands-on experience using GROMACS tools, simulation setup, data analysis, and visualization techniques.
The program also introduces web-based resources like CHARMM-GUI and covers workflows for real-world biomolecular systems. This workshop is ideal for students, researchers, and professionals from chemistry, biology, physics, and computational sciences seeking to enhance their skills in molecular simulation.
Target Audience
Students, Researchers and faculty members of Biology, Chemistry, Physics and material science
Key Topics:
Introduction to MD Simulations
Installation & Workflow
Analysis and Visualization
Protein-Ligand Simulations
Protein-Metal Complex/Nanomaterial Simulations
Features
Step-by-step Simulation Workflows
Assignments and Practical Exercises
Recordings will be available.
- eCertificate will be provided
Optional HPC Access
Participants can avail remote High-Performance Computing (HPC) access for 1 month to run their simulations efficiently with a nominal fee of Rs. 2500.
Recordings & Certificate
- Recordings of live sessions will be available for future reference.
- Participants will receive an e-certificate of completion.
Course Plan
Please download the course plan from the link provided below.
Schedule
Two-Week Workshop on GROMACS
Day & Time
Session
Topics
Link
- Day 1, 07.30 pm
- Introduction to Molecular Dynamics (MD)
- Introduction to MD simulations: Numerical recipe for running MD simulations, basic algorithm, software used for MD simulations
- Aim and information obtained from MD simulations
- Introduction to basics of high-performance computing (HPC)
- Introduction to the 'inSilicoLab' HPC system and its function, running jobs, allocation of resources, file sharing protocols, installed software packages, location of the software executables
- Day 2, 07.00 pm
- Introduction to Gromacs
- Introduction to Gromacs MD simulation package
- How to install Gromacs on Ubuntu OS, (for Windows OS, installing Ubuntu on a virtual machine and installing gromacs there), how to install gromacs for cpu only and gpu machines
- Workflow for running MD simulations in gromacs
- Introduction to files, file formats, units, constants in gromacs
- Basics of protein structure (primary, secondary & tertiary), structure file formats (gro file, pdb file), RCSB data bank, uniport, how to download pdb file
- Day 3, 07.30 pm
- Calculations using Gromacs
- Setting up a protein in water simulation (ubiquitin, lysozyme protein in water) in gromacs
- Step-by-step guide and hands-on workflow of using gromacs to setup protein in water simulation
- Running MD simulation on HPC server from command prompt and job script
- Day 4, 07.30 pm
- Analysis of the MD simulation data
- Analysis of the MD simulation data using gromacs tools
- Visualization of simulation trajectories using VMD
- Assignment for ubiquitin simulation
- Day 5, 07.30 pm
- Accessing GUI-based software tools on the server
- Introduction to web-based tools (e.g. Charmm-gui) for input preparation
- Preparing lipid-bilayer or membranes using charmm-gui
- Introduction to MD simulation setup of membrane-protein in water
- Preparing peptide-membrane simulation system
- Day 6, 07.30 pm
- Introduction to protein-ligand MD simulations in Gromacs
- Obtaining protein and Ligand parameters
- Running protein-ligand MD simulations
- Introduction to free-energy calculations
- Day 7, 07.30 pm
- Protein-Metal Complex MD simulations in Gromacs
- Obtaining protein and Ligand parameters
- Running protein-ligand MD simulations
- Day 8, 07.30 pm
- Protein-Nanomaterials MD simulations in Gromacs
- Obtaining protein and Ligand parameters
- Running protein-ligand MD simulations
- Day 9, 07.30 pm
- Analysis of the results
- Obtaining protein and Ligand parameters
- Running protein-ligand MD simulations
- Day 10, 07.30 pm
- Doubt-Clearing Session
- Doubt-Clearing Session
Resource Persons
Dr. SM Abdul Fayaz
Associate Professor
Department of Biotechnology
Manipal Institute of Technology (MIT)
Manipal Academy of Higher Education (MAHE),
Manipal
Dr. Bibhab Majumdar
Assistant Professor
Department of Chemistry
School of Advanced Sciences, VIT-AP University, Amaravati, Andhra Pradesh
Registration
Registration Fee
For Indian Participants: Rs. 3000
Foreign Participants: USD 50
SIAS Research Forum Members
Student Member: Rs. 2700
Faculty Member: Rs. 2400
HPC Charge: Rs. 2500 (optional)
Feedback from the participants
We will update this part after the compltion of the workshop!