Tag
Molecular Dynamics
Molecular Modeling How to Restart or Extend a GROMACS MD Simulation After a Crash or Timeout Restart a crashed GROMACS run from its checkpoint and extend a short one with gmx convert-tpr. Learn the exact commands and fix… 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 What Computer Do You Need for Molecular Docking and MD Simulations? (Laptop, GPU and Free Cloud Options) Check what hardware molecular docking and MD really need: laptop specs, why GROMACS wants a CUDA GPU, and the free Colab and… Dr. Abdul Rajjak Shaikh 12 min read Updated Molecular Modeling Molecular Docking vs Molecular Dynamics: What’s the Difference, and Do You Need Both? Compare molecular docking and molecular dynamics: what a pose proves, what a trajectory adds, and why a defensible thesis project runs both… Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling How Long Should You Run an MD Simulation? (And How to Know It Has Equilibrated) Pick a defensible MD simulation length and prove equilibration from RMSD, energy, temperature and pressure plateaus. Read the decision guide. Dr. Abdul Rajjak Shaikh 11 min read Updated 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