Topic
Molecular Modeling
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 Molecular Modeling How to Align and Superimpose Two Protein Structures in PyMOL (align, super and cealign): A Step-by-Step Guide Learn to superimpose two proteins in PyMOL with align, super and cealign, read the RMSD, pick the right command, and fix zero-atom… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling How to Plot GROMACS Results in Python from .xvg Files (RMSD, RMSF and Energy) Parse GROMACS .xvg files in Python and plot RMSD, RMSF and energy with a reusable read_xvg function. Start making publication-ready figures today. Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling How to Build a Free Energy Landscape from a GROMACS MD Trajectory Turn a GROMACS trajectory into a 2D free energy landscape with gmx sham and PCA. Start mapping your protein's conformational basins in… Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling How to Convert Molecular File Formats with Open Babel (PDB to PDBQT, MOL2 and SDF): A Beginner’s Guide Learn to convert PDB to PDBQT, MOL2, SDF and SMILES with Open Babel and get your docking files ready today. Dr. Abdul Rajjak Shaikh 9 min read Updated Molecular Modeling What Computer Do You Need for Molecular Docking and MD Simulations? (Laptop, GPU and Free Cloud Options) Check what hardware molecular docking and MD really need: laptop specs, why GROMACS wants a CUDA GPU, and the free Colab and… Dr. Abdul Rajjak Shaikh 12 min read Updated Molecular Modeling Molecular Docking vs Molecular Dynamics: What’s the Difference, and Do You Need Both? Compare molecular docking and molecular dynamics: what a pose proves, what a trajectory adds, and why a defensible thesis project runs both… Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling How to Choose a Protein Target and Ligands for a Molecular Docking Study (Step-by-Step) Pick a defensible protein target and ligand set before you open AutoDock Vina. Follow the step-by-step selection checklist that survives a viva. Dr. Abdul Rajjak Shaikh 13 min read Updated 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