Tag
GROMACS
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 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 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 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 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 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