Overview¶
DROPPS 1.0 organizes a coarse-grained simulation study into four layers:
model construction creates molecular coordinates and topology terms;
system construction assembles molecules and defines the periodic box;
run preparation and execution validates inputs, creates a portable run file, and runs OpenMM; and
trajectory processing and analysis selects, transforms, checks, and quantifies saved configurations.
The public interface is the dps command. Version 1.0 registers 28
subcommands. The accompanying article focuses on the central simulation and
analysis workflow, while this website also documents retained auxiliary and
migration commands.
Design principles¶
- Explicit files
Structures, topologies, parameters, run inputs, trajectories, energy data, index groups, and analysis products remain inspectable files.
- Early validation
dps grompp checks topology consistency and geometric constraints before a production job starts.
- Portable run inputs
TPR v2 stores the OpenMM System as XML and other data in JSON or NumPy representations instead of Python object pickles.
- Reproducible construction
Stochastic construction commands expose their seeds, with a documented default of 1215.
- Restart safety
dps mdrun writes native and portable restart information and checks its relationship to the run input.
Implementation¶
DROPPS is distributed as a Python package and uses OpenMM for molecular dynamics. MDAnalysis, NumPy, SciPy, pandas, Biopython, GSD, tqdm, and openpyxl support trajectory, analysis, and data-handling workflows. The release is licensed under the Apache License 2.0.