Tag
GROMACS
Molecular Modeling How to Calculate a Binding Free Energy with Umbrella Sampling in GROMACS (Pulling, Windows and gmx wham) Learn how to run umbrella sampling in GROMACS: set up the pull code, pick windows that overlap, run gmx wham and read… Dr. Abdul Rajjak Shaikh 18 min read Updated Molecular Modeling How to Analyze a GROMACS Trajectory in Python with MDAnalysis: A Step-by-Step Guide for Beginners Load a GROMACS .tpr and .xtc into MDAnalysis, reproduce RMSD and RMSF in Python, and write the per-frame analysis no gmx tool… Dr. Abdul Rajjak Shaikh 20 min read Updated Molecular Modeling How to Analyze Protein Secondary Structure from a GROMACS Trajectory (gmx dssp): A Step-by-Step Guide Run gmx dssp on your GROMACS trajectory, read the .dat and .xvg outputs, and fix the "do_dssp not found" error that breaks… Dr. Abdul Rajjak Shaikh 13 min read Updated Molecular Modeling How to Make a Point Mutation in a Protein Structure and Compare It with the Wild Type (PyMOL Mutagenesis + GROMACS) Mutate a residue in PyMOL, save the mutant correctly, then run a fair wild-type vs mutant MD comparison in GROMACS without overclaiming… Dr. Abdul Rajjak Shaikh 14 min read Updated Molecular Modeling How to Set Up a Membrane Protein MD Simulation with CHARMM-GUI and GROMACS Build a protein-in-bilayer system with CHARMM-GUI Membrane Builder, then run the six-step equilibration ladder in GROMACS without rebuilding anything. Dr. Abdul Rajjak Shaikh 13 min read Updated Molecular Modeling How to Define the Simulation Box in GROMACS with gmx editconf (Cubic vs Dodecahedron): A Step-by-Step Guide Set your GROMACS simulation box with gmx editconf. Choose cubic or dodecahedron, pick the right -d distance, and cut roughly 29 percent… Dr. Abdul Rajjak Shaikh 13 min read Updated Molecular Modeling How to Use gmx cluster: Extract a Representative Structure from a GROMACS Trajectory Learn to run gmx cluster with the gromos method and pull one defensible representative structure from your GROMACS trajectory. Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling How to Use gmx trjconv: Fix PBC and Extract Frames from a GROMACS Trajectory Learn the exact gmx trjconv commands to remove PBC artifacts, center your protein, strip water, and extract single frames before you run… Dr. Abdul Rajjak Shaikh 10 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 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