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 Analyze Radius of Gyration, SASA and Hydrogen Bonds from a GROMACS Trajectory (Step-by-Step) Measure compactness, solvent exposure and H-bonds from a GROMACS trajectory with gmx gyrate, gmx sasa and gmx hbond. Start analyzing your MD… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling How to Parameterize a Small-Molecule Ligand for a GROMACS Simulation: CGenFF vs ACPYPE vs ATB Learn how to build a GROMACS-ready ligand topology. Compare CGenFF, ACPYPE and ATB, then prepare a defensible protein-ligand system step by step. Dr. Abdul Rajjak Shaikh 9 min read Updated Molecular Modeling How to Choose a Force Field for Your GROMACS Simulation (CHARMM36 vs AMBER vs OPLS) Decide which force field to pick at the GROMACS pdb2gmx step. Compare CHARMM36, AMBER and OPLS, and learn to justify your choice… Dr. Abdul Rajjak Shaikh 9 min read Updated Uncategorized How to Analyze RMSD and RMSF from a GROMACS MD Trajectory (Step-by-Step) Calculate backbone RMSD and per-residue RMSF from a GROMACS trajectory with gmx rms and gmx rmsf, then read the plots. Start analyzing… Dr. Abdul Rajjak Shaikh 10 min read Updated 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
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