Molecular Simulation: Where Code Meets Chemistry

We are thrilled to bring you an event where code meets chemistry! Dive into how simulations and computational thinking tackle real molecular problems. If you want to see how molecules and orbitals look through equations by computation, this hands-on workshop is especially for you.

Event Details

• Speaker: Shuvam Banerjee Seal (22MS DCS)
• Venue: G06, Lecture Hall Complex
• Timing: 2:00 PM – 5:00 PM
• Requirements: Your curiosity! (Optional: Your laptop if you want to dive in hands-on)

Topics Covered

This comprehensive three-hour talk provided a bird's-eye view of the end-to-end molecular simulation workflow, covering:

1. Introduction to Molecular Simulation: Simulation, Molecular Modeling, Computational Experiments, Molecular Representation, Simulation Objectives, Applications.
2. Statistical Mechanics: Microstates, Macrostates, Phase Space, Energy, Entropy, Temperature, Free Energy, Boltzmann Distribution, Partition Function, NVE, NVT, NPT, Ergodicity, Ensemble Averaging.
3. Molecular Representation on Computers: Atomic Coordinates, Bonds, Angles, Dihedrals, Atomic Masses, Partial Charges, Simulation Box, Periodic Boundary Conditions, Potential Energy Surface, Force Fields.
4. Accuracy and Approximation in Simulation: Accuracy, Force-Field Approximations, Quantum Mechanics, Classical Mechanics, Parameterization, Numerical Errors, Sampling Errors, Accuracy–Cost Trade-off.
5. Time Scales in Molecular Simulation: Timestep, dt, Femtoseconds, Picoseconds, Nanoseconds, Microseconds, Simulation Length, Number of Steps, Molecular Timescales, Biological Timescales, Rare Events.
6. Static vs Dynamic Molecular Systems: Static Structures, Energy Minimization, Geometry Optimization, DFT, Potential Energy Minima, Thermodynamic Stability, Entropy, Solvent Effects, Free-Energy Landscape, Molecular Dynamics.
7. Molecular Dynamics: Newton’s Equations, Forces, Velocities, Positions, Numerical Integration, Initial Conditions, Trajectories, Equilibration, Production Runs, Sampling, Convergence.
8. Simulation Data Analysis: Trajectory Analysis, RMSD, RMSF, Radius of Gyration, Hydrogen Bonds, Distances, Angles, Radial Distribution Function, Conformational Clustering, Visualization, Statistical Analysis, Titan.
9. Enhanced Sampling and Free-Energy Methods: Sampling Problem, Rare Events, Metadynamics, Umbrella Sampling, Replica Exchange, Accelerated MD, Free Energy, Potential of Mean Force.
10. Molecular Simulation Software: LAMMPS, GROMACS, OpenMM, NAMD, AMBER, CHARMM, VMD, PyMOL, OVITO, ChimeraX.
11. Hands-on LAMMPS Simulation: Installation, Input Scripts, Simulation Box, Atom Definition, Force Fields, Boundary Conditions, Timestep, Simulation Execution, Log Files, Trajectory Files, Output Analysis.
12. Introduction to GROMACS: Installation, Structure Files, Topology, Parameters, Energy Minimization, NVT, NPT, Production MD, Trajectory Analysis.
13. Programming for Molecular Simulation: Linux, Bash, Python, NumPy, SciPy, Matplotlib, Pandas, MDAnalysis, MDTraj, RDKit, C/C++, Fortran, CUDA, Workflow Automation.
14. AI and Molecular Structure Prediction: AlphaFold, OpenFold, Protein Structure Prediction, Sequence-to-Structure, Structure Prediction vs Simulation, NVIDIA NIM, AI-Assisted Molecular Modeling.
15. Git, GitHub and Reproducibility: Version Control, Git, GitHub, Repository Management, Commits, Branches, README, Documentation, Simulation Scripts, Analysis Scripts, Versioning, Reproducibility, Data Management.
16. End-to-End Molecular Simulation Workflow: Scientific Question, System Preparation, Molecular Model, Force Field, Parameterization, Energy Minimization, Equilibration, Production MD, Trajectory Generation, Data Analysis, Visualization, Interpretation, Reproducibility -- we will try to cover a bird's eye view of it.

Note: For those who attended or missed the session, you can find the complete live stream recording and GitHub repository linked above. Please take a moment to share your thoughts via the feedback form link to help us improve future workshops!