Training Programs
Workshop on
Molecular Dynamics Simulations
Date
05 -12 Aug 2024
Time
07.30 pm IST
About the Workshop
Join us for an intensive one-week online workshop on Molecular Dynamics (MD) Simulation using GROMACS or NAMD. This workshop is designed to provide a comprehensive understanding of the principles and practical applications of MD simulations in biomolecular research. Participants will learn how to set up and perform simulations, analyze the results, and gain insights into the dynamic behavior of molecular systems. The workshop will utilize open-source tools such as GROMACS or NAMD, VMD, and other essential software, making it accessible for researchers and students alike.
Target Audience
Students, Researchers and faculty members of biology, chemistry, physics who are interested in learning about molecular dynamics simulations.
Tools to be used
NAMD/GROMACS, VMD, and others (All open-source Tools)
Computer Configuration: Linux (preferred), macOS, or Windows
Recording for Future Referenece
All live sessions will be recorded and made available to participants, ensuring they have access to the content for future reference and continued learning.
Topics
Installation of software
Simulation of Protein (receptor) Structure and of Receptor-Ligand Complex and Analysis of Results
Course Completion Certificate
At the end of the workshop, participants will receive an e-certificate of completion, recognizing their effort and newfound skills in GROMACS and Molecular Dynamics.
Course Plan
Schedule
One-Weeek Workshop on Molecular Dynamics Simulation
Day & Time
Session
Topics
Link
- Day 1, 07.30 pm
- Theoretical principles related to MD Simulation
- Introduction to the fundamental concepts of molecular dynamics
- Force fields, integration methods, and the importance of time steps in simulations
- Installation of GROMACS or NAMD
- Day 2, 07.30 pm
- System Setup for Simulation
- Detailed walkthrough of preparing a system for MD simulation
- Selection and preparation of biomolecules, solvation, ion addition, and energy minimization
- Troubleshooting installation issues
- Day 3, 07.30 pm
- Simulation of Protein (receptor) structure
- Simulating protein structures
- Equilibrate the system and run production MD simulations
- Day 4, 07.30 pm
- Simulation of Receptor-Ligand complex
- Explore the dynamics of receptor-ligand interactions
- Docking and binding site analysis
- Conformational changes upon ligand binding
- Day 5, 07.30 pm
- Analysis of Results
- Methods and tools for analyzing MD simulation results
- Trajectory analysis, calculation of RMSD, RMSF
- Hydrogen bonds, and secondary structure analysis
- Visualization tools like VMD to interpret and present the findings effectively
- Day 6, 07.30 pm
- Assignment/ Q&A Discussion
- Doubt-Clearing Session
Resource Person
Assistant Professor Department of Biotechnology Manipal Institute of Technology (MIT) Manipal Academy of Higher Education (MAHE) Manipal, Karnataka, India
Registration
Registration Fee
For Indian Participants: Rs. 2500
Foriegn Participants: USD. 40
SIAS Research Forum Members
Student Member: Rs. 2250
Faculty Member: Rs. 2000
Feedback from the participants
We will update this part after the compltion of the workshop!