File formats

DROPPS 1.0 uses explicit, stage-specific file types.

Model and parameter inputs

.ff

DROPPS coarse-grained force-field definition.

.itp

Molecule topology, including bead properties and bonded interactions.

.top

System topology that references force-field and molecule definitions and declares the system composition.

.mdp

Human-readable simulation parameters. A maintained template is installed at dropps/share/templates/md.mdp.

.pdb

Coordinates, residue and chain identifiers, and orthorhombic periodic-box dimensions used for model preparation and coordinate export.

Run and trajectory data

.tpr

DROPPS portable run-input container. TPR v2 is a versioned ZIP container whose members include OpenMM XML, JSON, NumPy arrays, a manifest, and per-member checksums.

Important

A DROPPS TPR is not a GROMACS TPR, despite using the familiar suffix. Read it with DROPPS 1.0 tools.

.xtc

Compressed trajectory with coordinates, time, step, and periodic-box data.

.edr

DROPPS energy data consumed by dps energy.

.chk, .state.xml, .restart.json

Native checkpoint, portable state, and restart manifest produced together by dps mdrun.

Selections and outputs

.ndx

Named atom groups created or extended by dps make_ndx.

.xvg, .xpm, .dat, .csv

Text or matrix outputs used by analysis commands. Consult the relevant command page for columns, units, and optional companion files.

Legacy TPR conversion

DROPPS 1.0 can read a trusted legacy pickle TPR from the immediately preceding format generation and convert it:

dps convert-tpr -s legacy.tpr -o portable.tpr

Python pickle loading can execute code. Convert only files whose origin and integrity you trust. Older files referencing the original Atomtype class are unsupported and must be regenerated from their PDB, TOP/ITP, and MDP inputs.