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.
Career Guide Fully Funded Life Science PhD, Fellowship and Scholarship Deadlines: August 2026 Onwards 90 life science PhD, fellowship and scholarship deadlines, every one verified on the funding organisation's official page. Africa and Latin America are… Dr. Abdul Rajjak Shaikh 35 min read Updated Molecular Modeling How to Generate a GROMACS Topology with pdb2gmx: A Step-by-Step Beginner’s Guide Learn to run gmx pdb2gmx step by step, pick a force field and water model, and fix the "residue not found" error… Dr. Abdul Rajjak Shaikh 8 min read Updated Bioinformatics How to Download a Protein Structure from the RCSB PDB and Read the File Find, download, and actually read a protein structure from the RCSB PDB before you dock or run MD. Start your modelling workflow… Dr. Abdul Rajjak Shaikh 9 min read Updated Career Guide How to Become a Bioinformatician in India After BSc or MSc: A Practical Roadmap Four real routes into bioinformatics after a BSc or MSc in India, the exams that fund them, and the skills a hiring… Ragini Mishra 15 min read Molecular Modeling How to Perform Energy Minimization in GROMACS: A Step-by-Step Tutorial Run energy minimization in GROMACS with the exact em.mdp settings, grompp and mdrun commands, and convergence checks. Learn to read Fmax and… Dr. Abdul Rajjak Shaikh 10 min read Updated Career Guide Fully Funded Life Science PhD, Fellowship and Scholarship Deadlines: August 2026 Onwards 33 life science PhD, fellowship and scholarship deadlines, every one verified on the funder's official page. Check which close first and start… Dr. Abdul Rajjak Shaikh 24 min read Updated Molecular Modeling How to Solvate a Protein and Add Ions in GROMACS (gmx solvate and gmx genion), Step by Step Solvate a protein and add neutralizing ions in GROMACS with the exact gmx solvate, grompp and gmx genion commands. Fix the SOL… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling GROMACS NVT and NPT Equilibration: A Step-by-Step Guide for Beginners Run NVT then NPT equilibration in GROMACS with the exact commands, .mdp settings, and convergence checks. Learn why both phases matter and… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling How to Restart or Extend a GROMACS MD Simulation After a Crash or Timeout Restart a crashed GROMACS run from its checkpoint and extend a short one with gmx convert-tpr. Learn the exact commands and fix… Dr. Abdul Rajjak Shaikh 10 min read Updated Bioinformatics How to Predict B-Cell Epitopes with BepiPred and ABCpred: A Step-by-Step Guide Run BepiPred and ABCpred on the same antigen, read per-residue scores against the threshold, and keep only consensus peptides. Start with this… Ragini Mishra 15 min read
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