Tag
GROMACS
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 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 How to Run an MD Simulation of DNA or RNA in GROMACS Learn exactly what changes when you simulate a nucleic acid instead of a protein in GROMACS: force field, ions, box and analysis. Dr. Abdul Rajjak Shaikh 17 min read Updated Molecular Modeling How Many Replicate MD Simulations Should You Run? Learn why one trajectory is not enough, how many replicas an MSc project needs, and how to run and report them in… Dr. Abdul Rajjak Shaikh 11 min read Molecular Modeling How to Write a Molecular Docking and MD Results Section Report docking and MD results the way examiners expect: the affinity table, the redocking control, which plots earn a figure, and standalone… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling DCCM Analysis of a GROMACS Trajectory, Step by Step Compute and read a dynamic cross-correlation matrix from a GROMACS run with Bio3D, ProDy or NumPy. Follow the exact commands and fix… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling Per-Residue Energy Decomposition with gmx_MMPBSA Turn one MM-GBSA number into a per-residue breakdown. Set up the decomp namelist, read the output and name your hotspot residues with… Dr. Abdul Rajjak Shaikh 15 min read Molecular Modeling GROMACS and AutoDock Vina on Mac: Apple Silicon Setup Install GROMACS, AutoDock Vina, Open Babel and PyMOL natively on an Apple Silicon Mac. No Rosetta, no MGLTools. Follow the verified setup. Dr. Abdul Rajjak Shaikh 13 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 gmx make_ndx Tutorial: Index Groups for Protein-Ligand MD Build Protein_LIG, ligand heavy-atom and pocket index groups with gmx make_ndx, script them, and fix the grompp group errors. Follow each step. Dr. Abdul Rajjak Shaikh 15 min read