GROMACS results: what a minimisation shows (pressure, step plots, energy format)
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 25/100
- Issue type
- Feature
- Clarity
- Mostly clear
- Activity status
- Active
- Tech stack
- c
- Domain
- data-visualization, desktop-dev
Research direction
Start in the Builder's Properties results view for a finished GROMACS minimisation, where pressure is shown as a full-height scalar panel, and in the Geometry Step Plots menu, which offers only Pressure and greys out the Y-axis. Done means that pressure is hidden for EM, potential energy and Fmax are selectable against step, step-click is active only when frames exist, and energies use significant figures with kJ/mol. Design choices are still open, so confirm them with maintainers (#180, #262, #241) before coding.
Written by the indexing model from the issue text.
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 (#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.
For the GROMACS round (#262/#241). Related: #180.
- Dominant language
- C
- Stars
- 10
- Forks
- 8
- Avg merge
- 21m
- Merged PRs (30d)
- 1
Getting set up
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First steps
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