Training Program on GROMACS Molecular Dynamics MD

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 and Brochure from the links provided below.
Schedule
Two-Week Workshop on GROMACS
Day & Time
Session
Topics
Link
- Day 1, 07.00 pm
- Introduction: Background Theory
- Introduction: Basic concepts in electrochemistry
- polarizable and non-polarizable electrodes, electrical double layer models, Nernst equation
- Electrochemical Techniques: Voltammetry, Amperometry, Potentiometry and Impedance spectroscopy
- Day 2, 07.00 pm
- Electrochemical Impedance Spectroscopy
- The Bode Plot
- The Nyquist Plot
- How EIS data is used
- Day 3, 07.30 pm
- Demonstration of CV Workstation
- Demonstration of CV Workstation
- Day 4, 07.30 pm
- Batteries & Supercapacitors: Introduction
- Applications of energy storage
- Energy storage technologies
- Trends in energy storage
- Advanced materials and technologies for supercapacitors
- Day 5, 07.30 pm
- Batteries: Measurement and Data analysis
- Performance indicators
- Data analysis
- Day 6, 07.30 pm
- Supercapacitors: Measurement and data analysis
- Performance indicators
- Day 7, 07.30 pm
- Electrocatalysis
- Introduction to Electrocatalysis
- Hydrogen Evolution Reactions (HER)
- Oxygen Evolution Reactions (OER)
- Day 8, 07.30 pm
- Measurement and Data analysis of electrocatalysis
- Performance indicators
- Day 9, 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!