Tag
Molecular Dynamics
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 PyMOL vs VMD vs ChimeraX: Which Should You Learn? Pick your molecular visualization tool by the job it does. Compare PyMOL, VMD and ChimeraX on licence, platforms and scripting before you… Dr. Abdul Rajjak Shaikh 13 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 PyMOL Commands for Docking and MD: Beginner Cheat Sheet Learn the PyMOL commands docking and MD students use every week, from binding-site selections to polar contacts and ray-traced figures. Start here. Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling How to Pick the Best Compound After Docking and MD Stop ranking hits on the Vina score alone. Build a defensible shortlist using ligand efficiency, filters and four MD criteria your examiner… Dr. Abdul Rajjak Shaikh 10 min read Molecular Modeling AlphaFold pLDDT and PAE Scores: Is Your Model Good Enough? Read pLDDT from the B-factor column and the PAE plot, then apply a clear go/no-go rule for docking or MD. Learn which… Dr. Abdul Rajjak Shaikh 13 min read