One Month International Bioinformatics Workshop on - Advanced MD Simulation & DFT - August 2026 3rd Edition by Decode Life
Registration is open for one month Bioinformatics Workshop by DE<code>LIFE
Duration : 5 August - 30 August 2026
Fees: Rupees 1300 for Indian Participants /USD 30 for International Participants.
Timing : 7. 30 PM Indian standard time.
Schedule
S.No | Day | Date | Topic |
1 | Wednesday | 05-Aug-2026 | Introduction to MD Simulation Analysis - Overview of MD Simulations - Importance of Post MD Simulation Analysis - Common software tools and packages for analysis |
2 | Thursday | 06-Aug-2026 | Data Preparation and Cleaning - Data file formats (e.g., XTC) - Data preprocessing and cleaning - Handling missing or corrupted data |
3 | Friday | 07-Aug-2026 | Trajectory Analysis - Extracting information from MD trajectories - Calculating structural parameters (RMSD, RMSF) - H-Bond Calculation - Center of Mass Distance |
4 | Saturday | 08-Aug-2026 | OFF |
5 | Sunday | 09-Aug-2026 | OFF |
6 | Monday | 10-Aug-2026 | Free Energy Calculations - Overview of free energy methods (e.g., MM/PBSA, MM/GBSA) - Performing binding free energy calculations |
7 | Tuesday | 11-Aug-2026 | Principal Component Analysis (PCA) - Understanding PCA and its applications in MD analysis - Plotting PCA |
8 | Wednesday | 12-Aug-2026 | Umbrella Sampling MD Simulation - Theoretical Basis of Umbrella Sampling - Preparing for Umbrella Sampling - Running Umbrella Sampling Simulations - Analyzing Umbrella Sampling Data |
9 | Thursday | 13-Aug-2026 | Introduction to Coarse-Grained MD - Basics of coarse-graining: key concepts and benefits - Overview of popular force fields - Applications of coarse-grained MD in biomolecular simulations |
10 | Friday | 14-Aug-2026 | System Preparation for Coarse-Grained MD - Steps to map an all-atom system to a coarse-grained representation - Preparing input files |
11 | Saturday | 15-Aug-2026 | OFF |
12 | Sunday | 16-Aug-2026 | OFF |
13 | Monday | 17-Aug-2026 | Running Coarse-Grained MD Simulations - Workflow: energy minimization, equilibration, and production runs - Key considerations for coarse-grained simulations |
14 | Tuesday | 18-Aug-2026 | Analysis of Coarse-Grained Simulations & Applications - Extracting key metrics: area per lipid, bilayer thickness, self-assembly - Tools and methods for coarse-grained simulation analysis - Modeling protein-lipid and protein-protein interactions - Applications in large biomolecular complexes and self-assembly studies |
15 | Wednesday | 19-Aug-2026 | Introduction to Steered MD - Principles of Steered MD: applying external forces in simulations - Key applications: protein-ligand interactions, unfolding studies |
16 | Thursday | 20-Aug-2026 | Setting Up & Analysis of Steered MD Simulations - Configuring Steered MD simulations: reaction coordinates and force constants - Defining pulling paths and setting up input files - Analyzing force-distance profiles and calculating work done - Linking Steered MD results to physical properties (e.g., binding affinity) |
17 | Friday | 21-Aug-2026 | Advanced Techniques in Steered MD - Multi-directional pulling and dynamic force spectroscopy - Optimizing pulling velocities and force constants |
18 | Saturday | 22-Aug-2026 | off |
19 | Sunday | 23-Aug-2026 | off |
20 | Monday | 24-Aug-2026 | A brief intro to quantum chemistry & DFT - Classical vs. quantum methods - Electronic concept - Introduction to DFT |
21 | Tuesday | 25-Aug-2026 | DFT theory and practical aspect - Functionals - Basis sets - SCF - Entry to Computational Platform ORCA 6.1 |
22 | Wednesday | 26-Aug-2026 | Platform preparation - Graphical tools (ChemCraft and Avogadro) - Input file preparations - Understanding the coordinate concept - Live task |
23 | Thursday | 27-Aug-2026 | Calculations & Analysis - Running ORCA - Geometry optimization and Frequency analysis - Understanding the keywords - Energy calculation - Charge distribution |
24 | Friday | 28-Aug-2026 | Calculations & Analysis - HOMO-LUMO identification - Molecular Orbitals - Single-point refinement |
25 | Saturday | 29-Aug-2026 | Calculations & Analysis - Complex optimization - Binding energy-Free energy - Solvation model - Thermochemistry - TD-DFT study |
26 | Sunday | 30-Aug-2026 | Calculations & Analysis - Intro to GOAT Algorithm - automated reaction tool - Metal complex simulation - Use of ZORA |
Key Features:
E- Certificate of Participation.
Video recording and workshop material
Global expert course faculty from diverse Institutions.
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