solvate¶

solvate is a lightweight Python package for quickly building initial structures for molecular dynamics simulations. It is built on top of MDAnalysis, so it interoperates cleanly with the rest of the MDAnalysis ecosystem and supports every file format MDAnalysis can read or write.

It is inspired by tools such as GROMACS solvate, but exposes a small, scriptable Python API that is easy to compose with your own pre-processing pipeline.

Highlights¶

Geometric insertion — fill rectangular, cylindrical, or spherical regions with arbitrary molecules.
Fast solvation — the Solvate* variants use spatial tiling to populate large boxes orders of magnitude faster than naive insertion.
Specify n or density — ask for an exact number of molecules or a target number density; solvate figures out the rest.
Built-in water models — SPC/E, TIP3P, and TIP4P/ε are included; custom 3- and 4-site models are one function call away.
MDAnalysis-native — inputs and outputs are Universe objects, so writing to any supported format is a one-liner.

A 30-second example¶

import solvate

# A 30 Å cubic, empty box
box = solvate.models.empty([30, 30, 30, 90, 90, 90])

# Fill it with SPC/E water at ~1 g/cm^3 (≈ 0.033 molecules / Å³)
water_box = solvate.SolvatePlanar(box, solvate.models.spce(), density=0.033)

water_box.atoms.write("water_box.pdb")

User documentation