Tag
GROMACS
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 Drug Design Protein-Ligand Complex PDB from an AutoDock Vina Pose Turn the top AutoDock Vina pose into one clean protein-ligand complex PDB for GROMACS and figures, and fix the errors that follow.… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling GROMACS Topology File Explained: topol.top and .itp Files Read topol.top line by line, place ligand .itp files in the right order and fix the grompp topology errors students hit most.… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling Ramachandran Plot from a GROMACS Trajectory (gmx rama) Learn to run gmx rama on an MD trajectory, plot every frame as a phi/psi density in Python, and spot residues that… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling GROMACS Protein Cofactor Simulation: Heme, NAD+ and FAD Keep heme, NAD+ or FAD in your GROMACS run: check the force field first, then parameterize only what is missing. Follow the… Dr. Abdul Rajjak Shaikh 13 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