Guides and tutorials
Computational life sciences, explained step by step.
Real commands, real parameters, and the errors that actually catch people out. Written by researchers who use these tools.
Molecular Modeling How to Visualize a GROMACS Trajectory in VMD: A Step-by-Step Beginner’s Guide Open your first GROMACS trajectory in VMD, fix the jumping-protein artifact, style a cartoon view, and export a movie. Watch your simulation… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling Protein-Ligand MD Simulation in GROMACS: A Step-by-Step Tutorial for Beginners Turn a docked pose into a real protein-ligand trajectory in GROMACS. Build the ligand topology, solvate, equilibrate, and run. Start your MD… Dr. Abdul Rajjak Shaikh 12 min read Updated Career Guide 8 Molecular Dynamics Project Ideas for Your MSc Thesis (GROMACS) Eight scoped, finishable GROMACS molecular dynamics project ideas for an MSc thesis, each with a research question, deliverable, and difficulty. Pick yours… Dr. Abdul Rajjak Shaikh 9 min read Updated 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 Bioinformatics How to Install GROMACS: A Beginner’s Guide for Windows, Linux and Google Colab Install GROMACS the right way on Linux, Windows (WSL2), or free Google Colab. Follow the exact commands and run your first gmx… 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
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