4 Day International Virtual
Workshop cum Faculty Development Program
Molecular Dynamics Simulations in Bioscience Research
18-21 Nov 2026
Quaxon Bio & IT Solutions, is going to conduct it’s 84th international virtual workshop cum Faculty Development Program on Molecular Dynamics Simulation in Bioscience Research.
Date: 18-21 Nov 2026
Time: 7 to 9 PM Indian
Standard Time
**Seats will be filled based on first come first serve basis
Objective
The Workshop-FDP will introduce the skill of Molecular
Dynamics Simulation to the participants through lectures,
demonstration and one to one hands-on session. The objective of the workshop is
to familiarize the participants with theoretical as well as practical concept
of molecular dynamics simulation so that they can apply this technique in their
study and research.
The expected outcome is that the participants should be
able to conduct MD simulations using GROMACS for Protein-Ligand complex and
able to analyze the output.
Eligibility:
All
Bioscience/Botany/pharmacy/biotech/biochemistry/biophysics/Bioinformatics
students, faculties and research scholar are eligible for this event.(No prior
coding experience is required, must have basic computer skill on Windows)
Continue reading or visit website post
https://qbiits.org/md-simulation-workshop-fdp-nov-26/
World Wide Time Schedule
India, Sri Lanka: 7.00 PM
Central European Time: 2.30 PM
Washington DC: 8.00 AM, Canada: 9:30
AM Moscow: 4.00 PM,
South Africa: 3:30 PM, Dubai: 5.00 PM, Moroco:
2.30 PM ,
Bangkok: 8.30 PM, London: 1:30 PM Kuwait: 5.00 PM
Kindly Visit https://savvytime.com/ to know the starting time in
your country’s time zone
Platform: Virtual mode with recording
access
About the Theme
Molecular Dynamics (MD)
simulation is a computational technique used in molecular modelling
to study the dynamic behaviour of atoms and molecules over time. It provides
valuable insights into the behaviour and properties of complex systems at the
atomic level. Molecular simulations usually deployed to calculate or predict
properties and quantities that may be difficult to observe experimentally. This
technology is widely used in various scientific fields, such as chemistry,
bioscience, materials science, and physics, to investigate molecular
structures, conformational changes, thermodynamics, and kinetics of chemical
reactions and other properties.
GROMACS is one of the most important and widely used molecular
dynamics simulation software packages in computational bioscience because of
its high performance, accuracy, and user-friendly workflow. It enables
researchers to study the dynamic behavior, stability, and interactions of
biomolecules such as proteins, nucleic acids, and protein–ligand complexes at
the atomic level. GROMACS widely used in drug discovery, protein
structure–function analysis, enzyme mechanism studies, and vaccine design by
allowing realistic simulation of biological systems under physiological
conditions. Its efficient algorithms, support for multiple force fields, and
powerful analysis tools make it especially valuable for bioscience students,
research scholars, and faculty for both learning and advanced research
applications.
System Requirement
Must have Windows 10 or above with minimum 4 GB(WSL
option) RAM/Ubuntu/other Linux variants. No coding knowledge required
This method has a central importance in bioscience and pharmaceutical science and it became an indispensable tools in bioscience research. Some applications are
· Design and discovery of new drug molecules.
· Understanding the dynamics of protein folding process.
· Characterizing biomolecular interactions:
· Understanding molecular cause of disease and drug resistance in microbes
Tools to be used:
GROMACS, VMD and other open source tools
No mandatory requirement of Linux OS, but must have windows 10 or above
Detail Syllabus and schedule
DAY 1: Theory, Software
Installation & System Setup
• Introduction to Molecular Dynamics (MD) Simulation and
its applications
• Newton’s equations of motion and integration algorithms
• Introduction to force fields: AMBER, CHARMM and OPLS
• Periodic boundary conditions (PBC)
• Overview of energy minimization, equilibration and
production dynamics
• Installation of GROMACS and environment configuration
• System requirements and computational environment setup
• Introduction to protein–ligand complex selection from
PDB
DAY 2: Protein–Ligand System Preparation
• Protein structure cleaning and preprocessing
• Ligand preparation and topology generation
• Generation of protein topology files
• Defining simulation box and boundary conditions
• Solvation of the system using water models
• Addition of ions and system neutralization
• Energy minimization of the prepared system
• Introduction to simulation input parameters (MDP files)
DAY 3: MD Simulation Execution & Monitoring
• Equilibration using NVT ensemble (constant Number,
Volume and Temperature)
• Equilibration using NPT ensemble (constant Number,
Pressure and Temperature)
• Preparation of the protein–ligand system for production
MD
• Production MD simulation setup and execution
• Monitoring temperature, pressure and energy stability
• Understanding GROMACS output and trajectory files
(.xtc, .trr, .edr, .log)
• Visualization of MD trajectories using VMD/PyMOL
DAY 4: MD Trajectory Analysis, Interpretation &
Troubleshooting
• Introduction to MD trajectory analysis
• Structural stability analysis: RMSD (Root Mean Square
Deviation)
• Flexibility analysis: RMSF (Root Mean Square
Fluctuation)
• Compactness analysis: Radius of Gyration (Rg)
• Protein–ligand interaction analysis: Hydrogen bonds
• Energy analysis during simulation
• Visualization and interpretation of conformational
changes
• Common errors and troubleshooting in GROMACS
• Best practices and practical case studies
Key Takeaway
·
Complete practical based
training and hands-on-session
·
Designed for beginner to
advance level learners
·
No prior coding experience
required
·
Applicable for Both Linux and
Windows user
·
E-Certificate for all
participants
·
Session recording and video
tutorial for further practice
Payment and Registration
Step-1: Pay the fee using the
below link as per your category
Step-2: Fill-up the
registration form after payment, attach the screenshot of payment
PAYMENT
For Indian participants
For B.Sc./M.Sc. students and
PhD Scholar Rs.1000/-
PhD Scholar Rs.1100/-
For faculty/pdf/RA and other working professionals Rs.1200/-
Payment link for Indians
https://pages.razorpay.com/pl_NMC6iJUcHHr686/view
or for Alternative
payment kindly WhatsApp +91-9692521875
For international participants (other than India)
For students $20/-
PhD Scholar $25/-
For faculty/Post Doctoral Fellow and other working
professionals $30/-
Payment link for international participants
https://www.paypal.com/paypalme/Workshop334
Registration
Must Register After the Payment, Using Below Link
https://docs.google.com/forms/d/1l3MRHRDYHPA-Cw2MdVX_aefxDztoIA3MzKMUK-NInJ0/edit
About Us
Quaxon Bio & IT Solutions is a fastest growing EduTech start-up registered to Ministry of Micro, Small and Medium Enterprises, Govt. of India. We are acting as industry-academic interface by knowledge transformation and produce human resource equipped with next generation technology. We are conducting webinar, conference and workshop on with international participants across the globe for knowledge transformation. Our main objective is to provide cutting edge technical education at affordable price to everyone. This is going to be our 84th International event.
WhatsApp/ call us +91-9692521875
Write to us quaxonbiits@gmail.com
For details term and condition kindly visit webpost
https://qbiits.org/md-simulation-workshop-fdp-nov-26/
WhatsApp/Call: +919692521875
Quaxon Bio & IT Solutions, India
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