Getting started

PQSetup prepares PQ input packages in a local browser. It does not install or run PQ. Install PQ separately to validate deeply and to execute run.sh.

You can design and export packages without a detected calculator or PQ executable. Missing checks are reported instead of silently passed.

Requirements

  • Python 3.11 or newer

  • A PQ executable to validate and run the generated inputs

  • The calculator and supporting files required by the chosen method

Install

python3 -m venv .venv
source .venv/bin/activate
python -m pip install "git+https://github.com/MolarVerse/PQSetup.git"

From a local clone:

python -m pip install .

Node.js is only needed when changing the interface.

Open the interface

pqsetup

PQSetup opens a local page at 127.0.0.1:8888. To choose another port or avoid opening a browser:

pqsetup serve --port 8890 --no-browser

Create the first package

  1. Keep the water example, or import a structure.

  2. Choose molecular mechanics or one QM calculator.

  3. Set the sampling ensemble and duration. Add NVT equilibration if needed.

  4. Review optional coordinate preparation.

  5. Inspect every generated input, then create the package.

Presets are editable starting points, not validated production protocols.

Check the environment

pqsetup doctor

doctor reports the selected PQ executable and the external calculators that PQSetup can detect. To use a different executable:

pqsetup --pq-executable /opt/pq/bin/PQ doctor

The same path can be supplied through PQ_EXECUTABLE.

Run the package

Unpack the download on the machine where PQ and the calculator are available:

mkdir water-nvt
unzip water-nvt.zip -d water-nvt
cd water-nvt
./run.sh /opt/pq/bin/PQ

The launcher follows the recorded input order, writes output to run-logs/, and stops after the first failed or incomplete PQ run.

PQSetup does not submit a scheduler job. Transfer and submission remain under the user’s control.

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