Topic
Molecular Modeling
Molecular Modeling How to Predict a Protein Structure with AlphaFold (ColabFold, No Install): A Beginner’s Guide Fold your protein sequence with AlphaFold in ColabFold, free and no install. Learn to read pLDDT and PAE so you know if… Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling How to Write the Methods Section for a Molecular Docking Study Write a docking methods section a reviewer accepts. Get the reporting checklist plus a worked, copy-adaptable AutoDock Vina example. Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling How to Set the Grid Box in AutoDock Vina: Center and Size Explained (Step-by-Step) Set the AutoDock Vina grid box the right way: find the binding-site center, pick a box size in Angstroms, and stop guessing… Dr. Abdul Rajjak Shaikh 12 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 Do Principal Component Analysis (PCA) on a GROMACS Trajectory: Essential Dynamics for Beginners Run PCA on a GROMACS trajectory with gmx covar and gmx anaeig to extract the dominant collective motions. Start building thesis-grade figures… Dr. Abdul Rajjak Shaikh 11 min read Updated 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 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