PQSetup

Prepare and validate PQ simulation inputs in a local browser interface.

PQSetup builds the input package. PQ runs it.

Documentation · Getting started · Command line

Install

Python 3.11 or newer. The UI ships inside the package; Node.js is not required.

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

From a local clone (contributors):

python -m pip install .

Quick Start

pqsetup

Keep the water example, choose a method, review the inputs, download the package, then run it where PQ is installed:

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

Check what this machine can see:

pqsetup doctor
pqsetup --pq-executable /path/to/PQ doctor

Validate an existing input:

pqsetup validate run.in

See the documentation for server options, validation scopes, and complete setup examples.

Input

Structure	Extension	Handling
PQ restart	.rst	Preserves atom names, molecule types, and available velocities or forces
CIF	.cif	Read through ASE
XYZ	.xyz, .extxyz	Reads standard and extended XYZ data
Protein Data Bank	.pdb	Read through ASE
MOL / SDF	.mol, .sdf	Read through ASE
ASE trajectory	.traj	Read through ASE

Multi-frame ASE sources import the final frame. Structures without a cell receive a centered vacuum cell. Periodic coordinates follow PQ's origin-centered cell convention.

Workflow

Step	Result
System	Inspect coordinates, elements, periodic cells, and close contacts
Method	Configure molecular mechanics or one supported QM calculator
Conditions	Build NVE, NVT, or NPT sampling with optional NVT equilibration
Prepare	Wrap periodic atoms and optionally perturb perfect crystal symmetry
Review	Inspect every generated input before creating the package

PQSetup does not submit jobs or run the simulation.

Validation

PQSetup checks the structure, plan, required files, and generated inputs locally. When the selected PQ executable advertises machine-readable validation, PQSetup also checks the inputs with PQ.

Environment detection reports what is available. It does not establish that a method, force field, or protocol is scientifically suitable.

PQSetup writes inputs for the stable PQ v0.7.0 release.

Run Packages

File	Purpose
run-eq.in	Optional NVT equilibration
run-01.in … run-999.in	Sampling inputs and restart chain
Structure restart	Prepared coordinates under the selected start filename
run.sh	Fail-fast execution in the recorded order
pqproject.json	Plan, environment, provenance, warnings, and file hashes

Uploaded force-field files and calculator templates are included in the package.

Development

python -m pip install -e ".[test]"
npm --prefix frontend ci
python -m pytest
npm --prefix frontend test
npm --prefix frontend run build