Tag
Trajectory Analysis
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 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 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 Molecular Modeling How to Do Principal Component Analysis (PCA) on a GROMACS Trajectory: Essential Dynamics for Beginners Run PCA on a GROMACS trajectory with gmx covar and gmx anaeig to extract the dominant collective motions. Start building thesis-grade figures… Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling How to Analyze Radius of Gyration, SASA and Hydrogen Bonds from a GROMACS Trajectory (Step-by-Step) Measure compactness, solvent exposure and H-bonds from a GROMACS trajectory with gmx gyrate, gmx sasa and gmx hbond. Start analyzing your MD… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling How to Visualize a GROMACS Trajectory in VMD: A Step-by-Step Beginner’s Guide Open your first GROMACS trajectory in VMD, fix the jumping-protein artifact, style a cartoon view, and export a movie. Watch your simulation… Dr. Abdul Rajjak Shaikh 10 min read Updated