Repository navigation
GROMACS results: what a minimisation shows (pressure, step plots, energy format) #334
Description
Found 2026-10-15 viewing a finished GROMACS minimisation (MINFF clay, 10236 atoms) in the Builder's Properties.
- Pressure is shown for a minimisation as a single final value (2030.8600000000 Bar) in a full-height panel. Pressure during an energy minimisation has no physical meaning: there are no velocities, so no kinetic term. Drop it for EM. For MD, show pressure as a time series beside temperature and density, not as a scalar.
- Geometry Step Plots offers only Pressure vs step, and the Y-axis menu is greyed out. For EM the useful series are potential energy and maximum force (Fmax) against step, the convergence quantities.
- Clicking a point should show that step's structure only when frames exist. EM normally writes only the final structure, so without frames the plot should not look clickable.
- Animation belongs to MD trajectories (MD analysis for electrolytes: RDF, coordination numbers, residence times, diffusion, conductivity, transference number #180), with the plot cursor following the frame.
- Total energy is shown as -4514170.000000 kJoule/Mole: fixed decimals on a large value, and the unit is spelled kJoule/Mole. Use significant figures and kJ/mol.
- A scalar property should not take a full-height panel.
Activity
ohlincha commentedon Oct 15, 2026
Per-step maximum force does not exist (checked 2026-10-15): the Y-axis menu offers Pressure, Total Energy and Geometry Step only. GROMACS writes energies per step to the .log, but Fmax only once, at the end ("Maximum force = ..."). mdrun prints the per-step values ("Step= n, Dmax= ..., Epot= ..., Fmax= ..., atom= ...") only on stderr and only with -v.
Plan: gensub runs mdrun -v with stderr kept as a job output file; gromacs.desc gets a per-step Fmax vector from it; the step plot offers Fmax vs step (log scale), beside Epot vs step.
ohlincha commentedon Oct 15, 2026
Andy, 2026-10-15: separate one-line panels (Pressure, Energies) look odd. For MD and minimisation runs, collect everything in one MD Summary panel:
The single-value panels then go away for these runs.