Molecular Dynamics Simulations of Protein Structure using Gromacs
Unlock the Power of Molecular Simulations: Master GROMACS for Protein Structure Analysis!
Virtual / Online
Mentor Based
Moderate
3 Days (1.5 hours per day)
15 -April -2025
4:00 – 5:30 PM IST
About
Molecular dynamics (MD) simulations are computational methods that monitor the temporal evolution of interacting atoms and molecules through the numerical integration of Newton’s laws of motion. This enables researchers to examine the dynamics and behaviour of molecular systems, which are essential for comprehending biomolecular interactions and have significant implications in fields such as drug discovery, protein engineering, and structural biology. To address the increasing interest in learning MD simulations on Linux using GROMACS, a flexible, open-source software tool utilized for conducting molecular dynamics (MD) simulations, especially for biomolecular systems like proteins, lipids, and nucleic acids, which help researchers simulate the movement of atoms and molecules over time based on classical mechanics. The upcoming workshop on Molecular Modelling and Dynamics Simulations of Biomolecule Structure will provide participants with a distinctive learning opportunity, featuring recorded videos for future reference. Attendees will acquire both theoretical and practical skills in modelling biological molecules, solvating proteins, conducting minimization, equilibration, and simulations, as well as analysing the outcomes. Offering a thorough introduction to molecular simulation using GROMACS, the workshop blends theoretical knowledge with practical applications, presenting an invaluable chance for researchers and professionals to incorporate MD simulations into their work.
Aim
To facilitate the MD simulation of biomolecule to explore biological phenomena and the behaviour at the molecular level.
Workshop Objectives
- To analyse the dynamic characteristics of molecular systems such as proteins, lipids, and nucleic acids at an atomic scale, enabling researchers to gain insights into their structure, interactions, and behaviour, which ultimately assists in unravelling biological processes and developing novel therapeutics.
- To represent and examine the arrangement of molecules and how they evolve over time, which is essential for comprehending their function.
This workshop intends to provide an arena for students, faculty and researchers in discussing the following topics as well as to provide hands on training in the following key areas for the new drug development.
Workshop Structure
Day 1
Overview of Protein and their energy level
- Overview of protein 3D structure file format
- Force field and Energy minimization
Overview of Molecular Dynamics Simulation
- Molecular Simulation and their types
- Molecular Dynamics Simulations
Day 2
Linux and Gromacs installation
- Installation of Ubuntu on Window
- Installation of Gromacs on Ubuntu
Molecular Dynamics Steps Using Gromacs
- Topology Generation, Define Box and Solvate, Add Ions, Energy Minimization, Equilibration, Production MD
Day 3
Protein Structure Simulation
- Protein structure Molecular Dynamics Simulation, Analysis of Results
Intended For
- Undergraduate/Postgraduate degree in Bioinformatics, Biotechnology, Biophysics, Computational Biology, or related fields.
- Researchers and professionals in pharmaceutical sciences, structural biology, or computational chemistry.
- Individuals with a keen interest in molecular modeling, drug discovery, and protein-ligand interactions.
Important Dates
Registration Ends
2025-04-15
Indian Standard Timing 3:00 PM
Workshop Dates
2025-04-15 to 2025-04-17
Indian Standard Timing 4:00 – 5:30 PM
Workshop Outcomes
- Understanding of molecular dynamics and protein structure simulations.
- Proficiency in using GROMACS for biomolecular simulations.
- Ability to analyze and interpret protein-ligand interactions.
- Skills in preparing simulation input files and running MD simulations.
- Hands-on experience with visualization and trajectory analysis tools.
Mentor Profile
Fee Structure
List of Currencies
FOR QUERIES, FEEDBACK OR ASSISTANCE
Key Takeaways
- Access to Live Lectures
- Access to Recorded Sessions
- e-Certificate
- Query Solving Post Workshop
Future Career Prospects
- Computational Biologist – specializing in molecular simulations and structural biology.
- Bioinformatics Scientist – focusing on drug discovery and protein modeling.
- Research Scientist in Biotechnology – utilizing MD simulations for protein structure analysis.
- Pharmaceutical Industry Analyst – working on computational drug design and virtual screening.
- Structural Bioinformatics Engineer – developing and optimizing biomolecular models.
- Academic Researcher – conducting advanced studies in molecular simulations and protein dynamics.
Job Opportunities
- Pharmaceutical Companies (Pfizer, Novartis, Roche, etc.)
- Biotech Startups & Research Institutions
- Academia & Universities (Postdoctoral and Research Assistant roles)
- Computational Drug Design & AI-driven Biotech Firms
- Healthcare and Biomedical Research Organizations
- Government and Private Bioinformatics Labs
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