Example data

The repository ships a checkout-only tutorial fixture under examples/water. It is an isolated water molecule in a 10 Å cubic cell (25 frames) plus the bundled H₂O Hessian. It exists so that the Python and CLI recipes can be copied and run; its numbers are not bulk-liquid data.

Get the files

Clone the repository (the fixture is not installed by pip):

$ git clone https://github.com/MolarVerse/PQAnalysis.git
$ cd PQAnalysis/examples/water

What is in the folder

File

Role

trajectory.xyz

25 PQ XYZ frames of one water molecule (O, H, H)

trajectory.vel

Matching velocity frames for VACF and momentum

restart.rst

Restart with the same topology (residue ids for exclusions)

moldescriptor.dat

H₂O residue template with partial charges

structure.rst / hessian.dat

Isolated-molecule Hessian fixture for vibrations

rdf.in, msd.in, vacf.in, vibrations.in

Input files sized to this 25-frame trajectory

msd.in and vacf.in use window = 8. Production trajectories need much larger windows; those keys are documented on the method pages.

Run the first RDF

$ pqanalysis rdf rdf.in

The table begins (trailing digits omitted):

# PQAnalysis: Radial distribution function
# FIELDS r_i g_r_i N_r_i g_r_i_dV_i H_i_minus_E_i
# SYMBOLS ...
# UNITS ...
0.25 0.0 ...
0.75 261.9 ...

The large \(g(r)\) near 0.75 Å is the intramolecular O–H peak. See RDF for column definitions.

The other commands in this folder are:

$ pqanalysis msd msd.in
$ pqanalysis vacf vacf.in
$ pqanalysis vibrations vibrations.in
$ pqanalysis check_momentum trajectory.vel \
    --selection all --output momentum.dat

Python recipes that load these files are on Learn the Python API; a continuous session from loading to a figure is on From trajectory to figure.