Troubleshooting

Start in Output → Review. It lists blocking errors and warnings for the current structure, method and run plan. Select an issue to jump to the relevant control; the input preview is unavailable until the blocking errors are resolved.

Package is disabled

Check the issue count beside Package and resolve every error in Review. Common causes are a missing structure or method file, an invalid run value, or a generated restart name that collides with an input file. If you changed the interaction model or ensemble, review the visible fields again: PQSetup remembers earlier choices but writes only settings that apply to the current selection.

PQ is not local

PQSetup can prepare a package without PQ. Local preflight still runs, but PQ parser validation is unavailable and is reported as such. On the machine that will run the simulation, inspect the environment and validate an input:

pqsetup --pq-executable /path/to/PQ doctor
pqsetup --pq-executable /path/to/PQ validate run-01.in

If that PQ build does not advertise the parser validation contract, PQSetup reports that limit. Review the inputs and test a short run with the intended calculator before committing to a long simulation.

Calculator or companion file is missing

The Method section reports local calculator discovery and shows the file slots required by the selected program or force field. Add the required topology, force-field or template files before packaging. A calculator that will only be available on another machine cannot be executed or scientifically checked by this machine; check it again at the destination with pqsetup doctor.

The downloaded package does not run

Extract the ZIP before running run.sh. Supply an executable PQ path, then inspect the log for the first failed input in run-logs/:

unzip water-nvt.zip -d water-nvt
cd water-nvt
./run.sh /path/to/PQ

The launcher stops at the first non-zero PQ exit or when PQ does not print its normal completion marker. It does not install PQ or the selected calculator. See Run packages for the input order and archive contents.

If a problem persists, include the PQSetup version, the selected PQ build, the Review message and a minimal input when opening an issue. Remove private structure or path data before sharing the files.