Tag
Molecular Dynamics
Molecular Modeling How to Run an MD Simulation of a Vaccine Construct-TLR Complex in GROMACS: Setup, Length and What to Report Take a docked vaccine construct into GROMACS: which pose to carry forward, force field and box setup, how many replicas to run,… Ragini Mishra 17 min read Molecular Modeling How to Fix Missing Residues and Loops in a PDB Structure Before Docking or MD (ChimeraX, SWISS-MODEL and MODELLER) Find the gaps your crystal structure never resolved, decide which ones matter, and rebuild them in ChimeraX, SWISS-MODEL or MODELLER before docking… Dr. Abdul Rajjak Shaikh 15 min read Molecular Modeling How to Analyze Protein-Ligand Interactions Over an MD Trajectory (ProLIF and MDAnalysis, Step by Step) Compute which binding-site residues held your ligand and for what percentage of the run, using ProLIF and MDAnalysis on a PBC-corrected GROMACS… Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling How to Calculate a Binding Free Energy with Umbrella Sampling in GROMACS (Pulling, Windows and gmx wham) Learn how to run umbrella sampling in GROMACS: set up the pull code, pick windows that overlap, run gmx wham and read… Dr. Abdul Rajjak Shaikh 18 min read Updated Molecular Modeling How to Analyze a GROMACS Trajectory in Python with MDAnalysis: A Step-by-Step Guide for Beginners Load a GROMACS .tpr and .xtc into MDAnalysis, reproduce RMSD and RMSF in Python, and write the per-frame analysis no gmx tool… Dr. Abdul Rajjak Shaikh 20 min read Updated Molecular Modeling How to Analyze Protein Secondary Structure from a GROMACS Trajectory (gmx dssp): A Step-by-Step Guide Run gmx dssp on your GROMACS trajectory, read the .dat and .xvg outputs, and fix the "do_dssp not found" error that breaks… Dr. Abdul Rajjak Shaikh 13 min read Updated Molecular Modeling How to Predict the Effect of a Mutation on Protein Stability (DynaMut2, mCSM and DDMut): A Step-by-Step Guide Predict how a point mutation changes protein stability with DynaMut2, mCSM and DDMut, and learn to read the ddG sign correctly before… Dr. Abdul Rajjak Shaikh 17 min read Updated Molecular Modeling How to Make a Point Mutation in a Protein Structure and Compare It with the Wild Type (PyMOL Mutagenesis + GROMACS) Mutate a residue in PyMOL, save the mutant correctly, then run a fair wild-type vs mutant MD comparison in GROMACS without overclaiming… Dr. Abdul Rajjak Shaikh 14 min read Updated Molecular Modeling How to Set Up a Membrane Protein MD Simulation with CHARMM-GUI and GROMACS Build a protein-in-bilayer system with CHARMM-GUI Membrane Builder, then run the six-step equilibration ladder in GROMACS without rebuilding anything. Dr. Abdul Rajjak Shaikh 13 min read Updated 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