Molecular Dynamics Simulation in Bioscience Research: From Theory to Practice
Explore Biomolecules in Motion—From Atomic Theory to Real Simulations.
About This Course
Molecular Dynamics simulation is a powerful computational technique that allows researchers to observe the dynamic behavior of biological molecules beyond static experimental structures. MD simulations provide insights into protein folding, conformational changes, ligand binding, membrane dynamics, and biomolecular interactions that are difficult to capture experimentally.
This workshop introduces MD simulation workflows used in bioscience, covering force fields, system preparation, energy minimization, equilibration, production runs, and trajectory analysis. Through dry-lab hands-on sessions, participants will learn to run and analyze simulations using standard MD tools, interpret trajectories, and connect simulation outcomes to biological function and experimental observations.
Aim
This workshop aims to train participants in the theoretical foundations and practical applications of Molecular Dynamics (MD) simulations in bioscience research. It focuses on understanding biomolecular motion, stability, and interactions at atomic resolution. Participants will learn how MD simulations are used to study proteins, nucleic acids, membranes, and biomolecular complexes. The program bridges fundamental theory with hands-on computational practice relevant to modern biological research.
Workshop Objectives
Participants will learn to:
- Understand the principles and assumptions behind MD simulations.
- Prepare biomolecular systems for simulation (proteins, complexes, solvents).
- Run energy minimization, equilibration, and production MD simulations.
- Analyze trajectories to extract biologically meaningful insights.
- Interpret simulation results in the context of experimental data.
Workshop Structure
Day 1: MD Foundations & System Setup
- MD in bioscience: use-cases (stability, mutation effects, binding, membranes)
- Essentials: force fields, solvation, PBC, NVT/NPT, minimization
- Hands-on tools: ChimeraX/PyMOL/VMD + GROMACS (or OpenMM/Colab)
- Mini task: Prepare protein → solvate + ions → energy minimization
Day 2: Running MD Correctly & Essential Analyses
- Equilibration workflow: restrained NVT → NPT → production basics
- Choosing force fields + quick ligand parameterization overview
- Key analyses: RMSD, RMSF, Rg, SASA, H-bonds
- Tools: GROMACS analysis (gmx rms/rmsf/gyrate/hbond/sasa) + MDAnalysis
- Mini task: generate RMSD/RMSF + H-bond occupancy and interpret
Day 3: Advanced Applications + Research-Grade Reporting
- Interaction insights: contacts, binding-site waters, clustering (states)
- Intro: MM/GBSA concepts + enhanced sampling overview (umbrella/metadynamics)
- Reproducibility: what to report + avoiding overclaims
- Tools: MDAnalysis/MDTraj (PCA/clustering) + optional PLUMED overview
- Mini task: 1-page MD mini-report (plots + conclusions + limitations)
Who Should Enrol?
- Doctoral Scholars & Researchers: PhD candidates seeking to integrate computational workflows into their molecular research.
- Postdoctoral Fellows: Early-career scientists aiming to enhance their data-driven publication profile.
- University Faculty: Professors and HODs interested in modern bioinformatics pedagogy and tool mastery.
- Industry Scientists: R&D professionals from the Biotechnology and Pharmaceutical sectors transitioning to genomic-driven discovery.
- Postgraduate Students: Final-year PG students looking for specialized research-grade exposure beyond standard curricula.
Important Dates
Registration Ends
01/08/2026
IST 07:00 PM
Workshop Dates
01/08/2026 – 01/10/2026
IST 08:00 PM
Workshop Outcomes
Participants will be able to:
- Understand and explain MD simulation workflows and concepts.
- Perform basic MD simulations of biomolecular systems.
- Analyze trajectories for structural stability and interactions.
- Interpret MD data to support biological hypotheses.
- Apply MD simulations in research, thesis projects, or industry workflows.
Fee Structure
Student Fee
₹1799 | $70
Ph.D. Scholar / Researcher Fee
₹2799 | $80
Academician / Faculty Fee
₹3799 | $94
Industry Professional Fee
₹4799 | $110
What You’ll Gain
- Live & recorded sessions
- e-Certificate upon completion
- Post-workshop query support
- Hands-on learning experience
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