Molecular Dynamics: Setup, Simulation & Analysis — Hands-on

Build confidence in setting up, running and analysing molecular dynamics (MD) simulations for biomolecular systems. This module walks through system preparation, solvation and ion placement, equilibration protocols, production simulations, trajectory quality checks and key analysis metrics so you can generate decision-grade MD results for structural biology and discovery projects.

Molecular Dynamics: Setup, Simulation & Analysis

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Session Index

Session 1 — System Building & Force Field Choices Session 2 — Equilibration Strategies & Production Runs Session 3 — Trajectory QC, Stability & Dynamics Analysis Session 4 — MD Workflows, Reproducibility & Case Study

Session 1

Fee: Rs 8800

System Building & Force Field Choices

From structure to simulation ready system

cleaning PDBs and repairing gaps protonation states & termini capping ligands, cofactors and metals overview

Force fields and water models in practice

major protein force fields landscape water and ion parameter choices consistency across complex, receptor, ligand

Solvation, ions and box setup

box shapes and system size neutralisation and salt concentration checking system composition and stoichiometry

Session 2

Fee: Rs 11800

Equilibration Strategies & Production Runs

Energy minimisation and early relaxation

removing bad contacts and clashes position restraints on heavy atoms monitoring potential energy behaviour

Temperature and pressure equilibration (NVT/NPT)

thermostats, barostats and coupling time step, constraints and cutoffs checking density, temperature and pressure

Planning robust production simulations

trajectory length and replication saving coordinates and velocities job submission and restart strategies

Session 3

Fee: Rs 14800

Trajectory QC, Stability & Dynamics Analysis

Quality control of MD trajectories

RMSD and equilibration windows temperature, pressure and energy trends detecting artefacts and instabilities

Stability and flexibility metrics

RMSF and per-residue flexibility radius of gyration and compaction secondary structure stability over time

Interactions, clustering and essential motions

H bonds, contacts and salt bridges clustering of conformations PCA / essential dynamics overview

Session 4

Fee: Rs 18800

MD Workflows, Reproducibility & Case Study

End-to-end MD case study: from PDB to analysis

Theory + Practical

Reproducible MD workflows and documentation

input files and parameter templates versioning scripts and configs notebooks and summary reports

Connecting MD results to project decisions

stability checks before docking / FEP figures and movies for presentations methods and limitations in manuscripts

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Molecular Dynamics Setup, Simulation & Analysis Training | From PDB to Trajectory Insights

Molecular Dynamics: Setup, Simulation & Analysis — Hands-on