Tag
MDAnalysis
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 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