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 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 Career Guide 15 Computational Biology Project Ideas for MSc & Final-Year Students (Docking + MD) 15 free computational biology project ideas (docking + MD) for MSc and final-year students. See what each proves to a PI and… Dr. Abdul Rajjak Shaikh 12 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
Weekly funding email
Get every new funding deadline by email
One email a week listing the funded PhD positions, fellowships and scholarships added that week, each one read from the funder's own website. Nothing else is sent.
Unsubscribe in one click from any email. We do not share your address, and we do not send anything else.
Learn this properly, live
A small-batch cohort in molecular modelling, docking and MD simulations, taught by researchers who publish. You run the full pipeline yourself.
See the next cohort