Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows
Fig 3
Intermediate results extracted from the “GROMACS Protein MD Setup” workflow.
(a) PDB structure with missing atoms added, ready to be used as MD input; (b) pressure and density box parameters measured over time in the final NPT equilibration process (10ps); (c) RMSd of the snapshots included in the final trajectory against the first snapshot (blue) and the original experimental structure (red); and (d) interactive visualization of the final trajectory using the simpletraj tool.