Build a run

PQSetup follows one direction: Structure, Method, Run, then Output. The table below is the control map; detailed scientific and format rules live in the linked references.

Control map

Area	Task	Check
Structure	Import a structure or run folder; inspect it in 3D; optionally apply seeded Jitter.	Confirm formula, atom count, cell, and close-contact warnings. A generated vacuum cell cannot be used for NPT.
Method	Choose QM or MM, select the calculator or force-field mode, and add the files shown under Files.	Detection reports software availability. It is not an energy, force, or dynamics calculation.
Run	Set the ensemble, initial velocities, coupling, timestep, sampling length, chained runs, resets, and optional equilibration.	Check that the physical protocol and total duration suit the system.
Output	Set the package name and output frequency; inspect Review and every tab under Inputs.	Errors block packaging. Warnings are recorded in pqproject.json.

Scientific checks

• The bundled water structure is one molecule in a generated vacuum cell.

• Imported trajectories use their final frame; the original file is unchanged.

• Generated cells use 6 Å of padding and are preparation aids, not convergence evidence.

• A hydrogen-containing structure above a 0.5 fs timestep is flagged for review.

• More than one sampling run creates run-01.in through run-NN.in; equilibration adds run-eq.in first.

Reference pages

• Compatibility lists structure formats, cell rules, calculators, and platform support.

• Advanced settings lists optional PQ keywords, constraints, and kinetic resets.

• Validation explains local preflight, environment discovery, PQ parser validation, and what those checks cannot prove.

• Run packages documents the archive, manifest, restart order, and launcher.

Shortcuts

Action	Shortcut
Search settings and issues	Ctrl+K / Cmd+K or /
Jump to Structure, Method, Run, or Inputs	Alt+1 through Alt+4
Create the package	Ctrl+Enter / Cmd+Enter
Close a dialog or search	Esc