Topic
Molecular Modeling
Molecular Modeling Your First GROMACS MD Simulation: A Step-by-Step Tutorial for Beginners Run your first protein MD simulation in GROMACS end to end, from PDB file to production trajectory. Follow the exact lysozyme-in-water commands… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling Molecular Docking on Google Colab: Run AutoDock Vina with No Installation Run molecular docking in your browser, set up AutoDock Vina in a free Google Colab notebook, dock from any laptop, and pull… Dr. Abdul Rajjak Shaikh 8 min read Updated Molecular Modeling How to Interpret Molecular Docking Results: Binding Affinity and Scores Explained Learn how to read molecular docking results, what the kcal/mol binding affinity means, why more negative is stronger, and how to prove… Dr. Abdul Rajjak Shaikh 9 min read Updated Molecular Modeling PyRx Tutorial for Molecular Docking: A Step-by-Step Beginner’s Guide Learn molecular docking in PyRx step by step, load your protein, prep ligands with Open Babel, run AutoDock Vina, and read binding… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling AutoDock Vina Tutorial for Beginners (Step by Step) Learn AutoDock Vina step by step, prepare files, set the grid box, run docking, and read binding affinity scores. Start your first… Dr. Abdul Rajjak Shaikh 9 min read Updated Molecular Modeling How to Prepare a Protein and Ligand for Molecular Docking (Step-by-Step Beginner’s Guide) Learn how to prepare a protein and ligand for docking, clean the PDB, add hydrogens and charges, and export PDBQT files. Get… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling Best Free Molecular Docking Software for Students (2026) Compare the best free molecular docking software for students in 2026 (AutoDock Vina, SwissDock, DiffDock). See costs, GPU needs and where to… Dr. Abdul Rajjak Shaikh 9 min read Updated Molecular Modeling Best Free Molecular Dynamics Software: GROMACS vs AMBER vs NAMD vs OpenMM (2026) Compare GROMACS, AMBER, NAMD, OpenMM and LAMMPS on license, GPU, and beginner-friendliness. See the best free MD engine for students and start… Dr. Abdul Rajjak Shaikh 9 min read Updated Molecular Modeling Molecular Docking vs Molecular Dynamics: What’s the Difference and Which Should You Learn First? Docking predicts where a molecule binds; molecular dynamics simulates how the complex moves. Key differences, when to use each, and which to… Dr. Abdul Rajjak Shaikh 9 min read Updated Molecular Modeling What Is Molecular Docking? A Beginner’s Guide A beginner's guide to molecular docking: what it is, how it predicts protein-ligand binding, why it matters for drug discovery, and how… Dr. Abdul Rajjak Shaikh 8 min read Updated