Tag
Molecular Dynamics
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 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 Molecular Modeling Protein-Ligand MD Simulation in GROMACS: A Step-by-Step Tutorial for Beginners Turn a docked pose into a real protein-ligand trajectory in GROMACS. Build the ligand topology, solvate, equilibrate, and run. Start your MD… Dr. Abdul Rajjak Shaikh 12 min read Updated Career Guide 8 Molecular Dynamics Project Ideas for Your MSc Thesis (GROMACS) Eight scoped, finishable GROMACS molecular dynamics project ideas for an MSc thesis, each with a research question, deliverable, and difficulty. Pick yours… Dr. Abdul Rajjak Shaikh 9 min read Updated Molecular Modeling Your First GROMACS MD Simulation: A Step-by-Step Tutorial for Beginners Run your first protein MD simulation in GROMACS end to end, from PDB file to production trajectory. Follow the exact lysozyme-in-water commands… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling Best Free Molecular Dynamics Software: GROMACS vs AMBER vs NAMD vs OpenMM (2026) Compare GROMACS, AMBER, NAMD, OpenMM and LAMMPS on license, GPU, and beginner-friendliness. See the best free MD engine for students and start… Dr. Abdul Rajjak Shaikh 9 min read Updated