15/06/2026
Day 10 of 10. Protein-ligand complex simulation complete. Workshop done. β
Ten days ago, participants were installing NAMD and VMD on Windows and making sure the files were in the right folder.
Today, they completed a full protein-ligand complex MD simulation in GROMACS β topology generation, ligand parameterisation via SwissParam, manual GRO file assembly in Notepad++, three precise topology file edits, position restraints on the ligand, energy minimisation, NVT, NPT, and a confirmed production MD run. Five output files. Ready for analysis.
And then one participant shared his screen and presented something that was not part of the workshop.
Working independently, he had taken the protocol from the previous nine days, applied it to the IEP kinase-imatinib complex β a real oncology drug target β and written approximately 800 lines of Python using the MDAnalysis library to generate a complete analysis package. Potential energy. RMSD for protein backbone and ligand separately. Per-residue RMSF. Radius of gyration. Hydrogen bond dynamics. Binding pocket maps. He is scaling it to 100 nanoseconds on Google Cloud Platform.
That is what ten days of genuine hands-on training looks like when it works.
Certificates will be issued within three working days.
π Online | Certificate Programme
π¬ NAMD Β· VMD Β· GROMACS Β· Linux Β· Windows
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