Tag
Molecular Dynamics
Molecular Modeling MD Simulation of a Protein-Protein Complex in GROMACS Take a docked or AlphaFold-Multimer complex through GROMACS, keep both chains whole, and test the interface with RMSD, contacts and H-bonds. Start… Dr. Abdul Rajjak Shaikh 15 min read Molecular Modeling MD Simulation at Different Temperatures in GROMACS Set up a 300 K vs 350 K vs 400 K thermal stability study in GROMACS, keep the runs comparable, and read… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling TIP3P vs SPC/E vs TIP4P: Which Water Model in GROMACS? Pick the water model your force field was built with. See the pairing rule, real property data and the exact pdb2gmx and… Dr. Abdul Rajjak Shaikh 12 min read 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 iMODS Tutorial: Normal Mode Analysis Step by Step Run iMODS normal mode analysis on a protein or docked complex, read every plot correctly, and avoid the input traps. Follow the… Dr. Abdul Rajjak Shaikh 12 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 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