01/27/2026

Registration closes 01/27/2026

Molecular Dynamics Simulation in Bioscience Research: From Theory to Practice

Explore Biomolecules in Motion—From Atomic Theory to Real Simulations.

  • Mode: Virtual / Online
  • Type: Mentor Based
  • Level:
  • Duration: 3 Days (1.5 Hours Per Day )
  • Starts: 27 January 2026
  • Time: 08:00 PM IST

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

01/27/2026
IST 07:00 PM

Workshop Dates

01/27/2026 – 01/29/2026
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.

Meet Your Mentor(s)

Mentor Photo

Prof. Kumud Malhotra

Professor & Dean

Prof. Kumud Malhotra, Dean of the University Institute of Physical and Life Sciences with 30 years of experience is an academician and administrator and has attained the highest echelons in the educational sector by managing senior positions, like Director, Dean, Managing Editor, or Editor-in-Chief . . . for content development and journal publication. She completed her Ph. D on “Genetic Epidemiology of Malaria in Some Population Groups of Delhi and Tribal Groups of Tarai Region of Nainital District” and Post Doctorate from Delhi University as an ICMR and UGC fellow.
Her expertise domains are Biotechnology, Genetics, Bioinformatics, Forensic  Science, Molecular Biology, and its allied areas. She has obtained Certifications in the areas of Genetic Engineering, Molecular Biology, Microarrays, Proteomics, and Parasitology from IGIB, NICD, MRC, and Delhi University. Down the lane, her achievements and accolades are the best employee and faculty while working at Bioinformatics Institute of India and RNB GLOBAL University as a Dean and other prestigious awards. Her contribution to the establishment of the School of Basic and Applied Sciences and Agricultural Sciences along with the approval from ICAR at the new University RNBGLOBAL
University was acknowledged by the Management.
Apart from teaching and academics her experience in content development and e-learning for various renowned universities and organizations like Banasthali Vidyapith, GOLS Academy, Biionline, etc. is an added credential of hers. Dr. Kumud Malhotra has been a Resource Person in Course Development Committees (for graduate and post-graduate programs) for Indira Gandhi National Open University (IGNOU), Jamia Hamdard along with other credits like Member of various committees like Academic Council, BOS, Research Committee, etc. for the IGNOU, IAMR. She has demonstrated caliber as a resourceful Technical Collaborator for the conduction of the Workshop on Bioinformatics at
Bundelkhand University and in Engineering College in Durg, Chhattisgarh with an appreciation letter from the university.
She is a member of the editorial board of various journals and has presented Papers at International Conferences on Genetics, Parasitology, Clinical Trials, Pharmacovigilance, Biotechnology, etc. Dr. Malhotra has delivered keynote addresses at CII, International Conferences, and member of various professional bodies Genetics Society, Indian Science Congress, International Society for Malariology and Parasitology, IAA, SBTI, etc. She has guided many students for Ph.D. and internships and got the projects from ICMR.

Fee Structure

Student Fee

₹1699 | $60

Ph.D. Scholar / Researcher Fee

₹2699 | $70

Academician / Faculty Fee

₹3699 | $85

Industry Professional Fee

₹4699 | $100

What You’ll Gain

  • Live & recorded sessions
  • e-Certificate upon completion
  • Post-workshop query support
  • Hands-on learning experience

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