Topic
Molecular Modeling
Molecular Modeling How to Define the Simulation Box in GROMACS with gmx editconf (Cubic vs Dodecahedron): A Step-by-Step Guide Set your GROMACS simulation box with gmx editconf. Choose cubic or dodecahedron, pick the right -d distance, and cut roughly 29 percent… Dr. Abdul Rajjak Shaikh 13 min read Updated Molecular Modeling How to Find a Protein’s Binding Site for Docking with fpocket, CASTp and PrankWeb Predict a protein's binding pocket with PrankWeb, fpocket or CASTp, then convert it into the grid box coordinates AutoDock Vina needs. Dr. Abdul Rajjak Shaikh 15 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 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