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Welcome to warp-md

warp-md is a Rust/CUDA/Python toolkit for molecular trajectory IO, analysis, packing, and peptide workflows. Built for performance and ease of use, it brings GPU-accelerated analysis to your molecular dynamics simulations.

Installation

Install via pip or build from source in minutes

Quickstart

Run your first analysis in 5 lines of code

API Reference

Explore the complete Python API

CLI Reference

Command-line tools for analysis and packing

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What You Can Do

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Trajectory Analysis

Run over 98 analysis plans including RMSD, radius of gyration, PCA, clustering, hydrogen bonds, radial distribution functions, GIST, DSSP, and many more. 
from warp_md import System, Trajectory, RgPlan

system = System.from_pdb("topology.pdb")
selection = system.select("protein")
traj = Trajectory.open_xtc("trajectory.xtc", system)
rg = RgPlan(selection).run(traj, system, device="auto")
print(rg[:5])

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Molecular Packing

Generate complex molecular systems with automatic clash avoidance. Pack water molecules, ions, ligands, and custom structures into simulation boxes. 
from warp_md.pack import Box, Structure, PackConfig, water_pdb
from warp_md.pack.runner import run
from warp_md.pack.export import export

cfg = PackConfig(
    structures=[Structure(water_pdb("tip3p"), count=200)],
    box=Box((40.0, 40.0, 40.0)),
    min_distance=2.0,
)
result = run(cfg)
export(result, "pdb", "packed.pdb")

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Peptide Workflows

Build, mutate, and manipulate peptide structures with the warp-pep CLI utility.

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Key Features

GPU Acceleration

Optional CUDA support for massive speedups on supported operations

98+ Analysis Plans

Comprehensive library of trajectory analysis methods

Flexible IO

Read PDB, XTC, and other common trajectory formats

Python + Rust

Python ergonomics with Rust performance

CLI Tools

Three command-line utilities: warp-md, warp-pack, warp-pep

YAML Configs

Run complex analysis workflows from configuration files

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Quick Example

Calculate radial distribution function from the command line: 
warp-md rdf \
  --topology top.pdb \
  --traj traj.xtc \
  --sel-a "resname SOL and name OW" \
  --sel-b "resname SOL and name OW" \
  --bins 200 \
  --r-max 10
Or use configuration files for reproducible workflows: 
warp-md example > config.json
warp-md run config.json
Run warp-md list-plans to see all 98+ available analysis plans and their parameters.

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Next Steps

1

Install warp-md

Follow the installation guide to get warp-md on your system
2

Run your first analysis

Complete the quickstart tutorial to analyze a trajectory
3

Explore analysis plans

Browse the API reference to discover available analysis methods

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