Tag
Computational Biology
Molecular Modeling How Long Should You Run an MD Simulation? (And How to Know It Has Equilibrated) Pick a defensible MD simulation length and prove equilibration from RMSD, energy, temperature and pressure plateaus. Read the decision guide. Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling How to Write the Methods Section for a Molecular Dynamics Study (GROMACS Example) Turn your GROMACS run into a methods section a reviewer cannot reject. The exact parameters to report, real citations, and a worked… Dr. Abdul Rajjak Shaikh 12 min read Updated Molecular Modeling The GROMACS .mdp File Explained: The Parameters That Actually Matter Stop copy-pasting em.mdp and md.mdp. Learn which GROMACS .mdp parameters you must choose deliberately, which to leave at defaults, and what breaks… Dr. Abdul Rajjak Shaikh 12 min read Updated Molecular Modeling Common GROMACS Errors and How to Fix Them (LINCS Warnings, PBC and ‘Atom Not Found’) Decode the GROMACS errors beginners actually hit: LINCS warnings, PBC artifacts, rtp mismatches and cut-off failures. Read the fix for each message. Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling How to Do Blind Docking with AutoDock Vina When You Don’t Know the Binding Site Learn to run blind docking in AutoDock Vina to find an unknown binding site, from sizing a whole-protein box to clustering poses.… Dr. Abdul Rajjak Shaikh 11 min read Updated Drug Design AutoDock Vina vs AutoDock4: Which Docking Tool Should a Beginner Use? Compare AutoDock Vina and AutoDock4 on scoring, speed, setup, and accuracy so you pick the right docking engine for your thesis. Read… Dr. Abdul Rajjak Shaikh 9 min read Updated Drug Design How to Make 2D Protein-Ligand Interaction Diagrams (LigPlot+ & PLIP): Step by Step Turn any AutoDock Vina or PyRx docking pose into a publication-ready 2D interaction diagram with free tools. Follow the LigPlot+ and PLIP… Dr. Abdul Rajjak Shaikh 9 min read Updated Drug Design 7 Molecular Docking Project Ideas for Your MSc Thesis (and Your CV) Pick a scoped, defensible molecular docking project you can finish with free tools and public data. Start building your thesis today. Dr. Abdul Rajjak Shaikh 7 min read Updated Molecular Modeling How to Run a GROMACS MD Simulation on Google Colab (Free GPU, No Install) Run a full GROMACS molecular dynamics simulation on Google Colab's free GPU, no local install. Set up the runtime, install GROMACS, and… 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