Tag
Trajectory Analysis
Molecular Modeling gmx rdf Tutorial: Radial Distribution Function in GROMACS Calculate a radial distribution function with gmx rdf: water, ions and binding-site solvation, coordination numbers and fixes. Run it on your trajectory. Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling Contact Map Analysis in GROMACS with gmx mdmat Build a residue contact map from a GROMACS trajectory with gmx mdmat, then a contact-frequency heatmap in MDAnalysis. Compare wild type and… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling Salt Bridge Analysis in GROMACS: gmx saltbr vs pairdist Track a salt bridge across a GROMACS trajectory with gmx pairdist, compute its occupancy in Python, and learn why gmx saltbr misleads.… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling gmx hbond for Protein-Ligand H-Bonds in GROMACS 2024+ Count protein-ligand hydrogen bonds with the new gmx hbond in GROMACS 2024+, or hbond-legacy. Copy the exact commands, get occupancy and read… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling Ligand RMSD in GROMACS: Fit, Fix PBC, Read the Plot Calculate ligand RMSD in GROMACS the right way: fit on the protein backbone, fix periodic jumps first, and learn to read stable,… Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling Wild-Type vs Mutant MD Simulation in GROMACS Design a wild-type versus mutant MD comparison in GROMACS that survives examination: matched protocol, replicas, and a difference you can defend. Dr. Abdul Rajjak Shaikh 16 min read Molecular Modeling Protein-Ligand Interaction Energy in GROMACS (Rerun Guide) Compute Coulomb and LJ protein-ligand interaction energy in GROMACS with energygrps, mdrun -rerun and gmx energy. Follow the exact commands. Dr. Abdul Rajjak Shaikh 13 min read 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 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