Examples

The examples directory contains complete input folders. Each example should be run from its own directory so relative setup-file paths resolve as intended.

Folder	Main use case	Notes
examples/h2o_mm	MM-MD water	Self-contained classical MD example using moldescriptor.dat and guff.dat.
examples/amyloid-classical	Classical force-field setup	Uses topology, parameter and intramolecular non-bonded setup files.
examples/umcm-9_dftb+	DFTB+ with SHAKE	Uses dftb_in.template and a topology file with SHAKE constraints.
examples/malondialdehyde_dftb+	DFTB+ QM-MD	Uses an external DFTB+ setup template.
examples/malondialdehyde_dftb+-rpmd	DFTB+ QM-RPMD	Ring-polymer MD example with DFTB+.
examples/malondialdehyde_pyscf	PySCF QM-MD	Uses the PySCF QM runner.
examples/malondialdehyde_tm-rpmd	Turbomole QM-RPMD	Uses a Turbomole define template.
examples/h2o_mace	MACE water	Small MACE example using qm_prog = mace_mp.
examples/acof1_mace	MACE solid-state MD	MACE example for a covalent organic framework with pressure coupling.
examples/mof-5_mace	Custom MACE model	Uses mace_model_path for a custom model URL.
examples/mof-5_ase-dftb	ASE-DFTB+	Uses the ASE DFTB+ runner and built-in Slater-Koster setup.
examples/mof-5_ase-xtb	ASE-xTB	Uses the ASE xTB runner with xtb-method.

Running an Example

After building PQ, run an example from the example directory:

$ cd examples/h2o_mm
$ ../../build/apps/PQ run-01.in

Most examples are configured for real simulations rather than minimal smoke tests. To make a quick local test, copy the example directory and lower nstep in the copied run-01.in.

Optional Dependencies

Examples using dftbplus, pyscf, turbomole, mace_mp, ase-dftbplus or ase-xtb require the corresponding external program or Python package to be available in the run environment. ASE-based examples also require PQ to be built with ASE support.