DROPPS 1.0

Distributed Rapid Operation Platform for Phase-separation Simulations

DROPPS is a command-line toolkit for building, running, and analysing coarse-grained biomolecular simulations. Version 1.0 provides a publication release centred on an OpenMM execution engine, portable run-input files, and reproducible command-line workflows.

The shortest route from a sequence to an analysis is:

1. build a molecular model with Quick start;

2. package validated inputs with dps grompp;

3. run or resume the simulation with dps mdrun; and

4. inspect or analyse the trajectory with the tools in Command reference.

Start here

Getting started

• Request DROPPS 1.0 access
  • License
• Installation
  • Requirements
  • Automated installation
  • Install the wheel
  • Verify the environment
• Quick start
  • 1. Build a single-chain model
  • 2. Pack the simulation box
  • 3. Prepare a portable run input
  • 4. Run and validate
  • 5. Create groups and analyse

User guide

• Overview
  • Design principles
  • Implementation
• Workflow
  • Molecular model
  • System model
  • Run preparation
  • Simulation and restart
  • Trajectory preparation
  • Analysis
• File formats
  • Model and parameter inputs
  • Run and trajectory data
  • Selections and outputs
  • Legacy TPR conversion
• Reproducibility and validation
  • Record the complete computational contract
  • Random seeds
  • Input validation
  • Floating-point scope
  • Diagnosing failures
• HPC execution
  • Prepare the environment
  • Portable staging
  • Example Slurm job
  • Continue a scheduled run
  • CPU execution

Command-line reference

• Command reference
  • Build a simulation system
  • Run or recompute a simulation
  • Inspect and convert files
  • Analyze structure and contacts
  • Analyze phase behavior and transport
  • CLI infrastructure

Project information

• DROPPS 1.0 release notes
  • Publication workflow
  • Reliability and portability
  • Interface
  • Distribution
• Citation
  • Software citation
  • Machine-readable metadata
• Support
  • Before opening an issue
  • Command discovery
• License

Version contract

These pages document DROPPS 1.0 only. Every command page is generated from the argument parser in the submitted 1.0 source tree. Use dps --version to confirm the installed release and dps help commands to list its commands.