Topic
Molecular Modeling
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 Molecular Modeling How to Solvate a Protein and Add Ions in GROMACS (gmx solvate and gmx genion), Step by Step Solvate a protein and add neutralizing ions in GROMACS with the exact gmx solvate, grompp and gmx genion commands. Fix the SOL… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling GROMACS NVT and NPT Equilibration: A Step-by-Step Guide for Beginners Run NVT then NPT equilibration in GROMACS with the exact commands, .mdp settings, and convergence checks. Learn why both phases matter and… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling How to Restart or Extend a GROMACS MD Simulation After a Crash or Timeout Restart a crashed GROMACS run from its checkpoint and extend a short one with gmx convert-tpr. Learn the exact commands and fix… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling How to Align and Superimpose Two Protein Structures in PyMOL (align, super and cealign): A Step-by-Step Guide Learn to superimpose two proteins in PyMOL with align, super and cealign, read the RMSD, pick the right command, and fix zero-atom… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling How to Plot GROMACS Results in Python from .xvg Files (RMSD, RMSF and Energy) Parse GROMACS .xvg files in Python and plot RMSD, RMSF and energy with a reusable read_xvg function. Start making publication-ready figures today. Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling How to Build a Free Energy Landscape from a GROMACS MD Trajectory Turn a GROMACS trajectory into a 2D free energy landscape with gmx sham and PCA. Start mapping your protein's conformational basins in… Dr. Abdul Rajjak Shaikh 11 min read Updated