Tag
GROMACS
Molecular Modeling How to Write the Methods Section for a Molecular Dynamics Study (GROMACS Example) Turn your GROMACS run into a methods section a reviewer cannot reject. The exact parameters to report, real citations, and a worked… Dr. Abdul Rajjak Shaikh 12 min read Updated Molecular Modeling The GROMACS .mdp File Explained: The Parameters That Actually Matter Stop copy-pasting em.mdp and md.mdp. Learn which GROMACS .mdp parameters you must choose deliberately, which to leave at defaults, and what breaks… Dr. Abdul Rajjak Shaikh 12 min read Updated Molecular Modeling Common GROMACS Errors and How to Fix Them (LINCS Warnings, PBC and ‘Atom Not Found’) Decode the GROMACS errors beginners actually hit: LINCS warnings, PBC artifacts, rtp mismatches and cut-off failures. Read the fix for each message. Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling How to Calculate Protein-Ligand Binding Free Energy in GROMACS (MM-PBSA Tutorial) Estimate protein-ligand binding free energy from a finished GROMACS trajectory with the free gmx_MMPBSA tool. Follow the step-by-step MM-PBSA workflow now. Dr. Abdul Rajjak Shaikh 9 min read Updated Molecular Modeling How to Prepare a Protein Structure for MD Simulation (Missing Residues, Hydrogens, Protonation) Learn to clean a raw PDB for MD: rebuild missing loops, add hydrogens, and fix His, Asp and Cys protonation so your… Dr. Abdul Rajjak Shaikh 12 min read Updated Molecular Modeling How to Run a GROMACS MD Simulation on Google Colab (Free GPU, No Install) Run a full GROMACS molecular dynamics simulation on Google Colab's free GPU, no local install. Set up the runtime, install GROMACS, and… Dr. Abdul Rajjak Shaikh 9 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 Parameterize a Small-Molecule Ligand for a GROMACS Simulation: CGenFF vs ACPYPE vs ATB Learn how to build a GROMACS-ready ligand topology. Compare CGenFF, ACPYPE and ATB, then prepare a defensible protein-ligand system step by step. Dr. Abdul Rajjak Shaikh 9 min read Updated Molecular Modeling How to Choose a Force Field for Your GROMACS Simulation (CHARMM36 vs AMBER vs OPLS) Decide which force field to pick at the GROMACS pdb2gmx step. Compare CHARMM36, AMBER and OPLS, and learn to justify your choice… Dr. Abdul Rajjak Shaikh 9 min read Updated