Build a run

PQSetup keeps the scientific setup in five visible steps. The preflight panel updates as the structure, method, and protocol change.

1. System

Import .rst, .cif, .xyz, .extxyz, .pdb, .mol, .sdf, or .traj. For a multi-frame trajectory, PQSetup imports the final frame.

The structure pass checks finite coordinates, element labels, the periodic cell, and unusually close contacts. Periodic coordinates are wrapped to fractional coordinates from −0.5 to +0.5. For an orthorhombic cell, that is −L/2 to +L/2. The original file is not modified.

Structures without a cell receive an orthorhombic cell with 6 Å of padding on each side. That generated cell is a convenient vacuum boundary, not a claim that the chosen dimensions are physically converged.

2. Method

Choose one interaction model:

• Molecular mechanics with GUFF, bonded plus GUFF, or a classical force field and the required topology or parameter files.

• QM molecular dynamics with one supported external calculator and any required templates.

PQSetup checks whether the selected calculator appears available in the current environment. This is a discovery check, not an energy or force calculation. A portable package can still be prepared for another machine when the local calculator is absent.

3. Conditions

Sampling can use NVE, NVT, or NPT. Temperature coupling, pressure coupling (manostat in PQ), timestep, target conditions, and run length remain editable.

Add an optional NVT equilibration stage, then write sampling as one input or a numbered restart chain. Every later input reads the previous restart.

An equilibration restart followed by three continued sampling inputs.

Why PQ says manostat

PQ uses manostat for the pressure-coupling algorithm. It is essentially the component most molecular-dynamics programs call a barostat.

4. Prepare

Periodic atoms stay wrapped in PQ’s centered-cell convention. For a perfect crystal, an optional seeded Gaussian position perturbation can break exact symmetry. The same seed reproduces the same coordinates.

Velocity initialization is performed by PQ at runtime. PQSetup writes the temperature and random seed; PQ samples the mass-dependent velocities and removes net motion.

5. Review

Review the run name, structure name, execution order, continuation files, and the complete text of every generated input. Errors block package creation; warnings remain visible and are recorded in the project manifest.

The restart relationship and final PQ input are visible before export.

The exported input header identifies PQSetup and the targeted PQ schema. It is designed to make provenance obvious without obscuring the settings that matter.

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