Google Colab tutorials¶
These five browser-based notebooks provide a guided route through DROPPS 1.0,
from the first model to phase-separation analysis. No local installation is
required. For simulations, select a GPU runtime in Colab with
Runtime > Change runtime type.
The original .ipynb files are hosted directly by dropps.online and are
available through each Download notebook button. Google Colab currently
limits one-click public-URL imports to supported hosts, so the Run in Google
Colab buttons use the matching immutable files in the official DROPPS
v1.0.0 GitHub release. Colab creates a working copy; save that copy to
Google Drive if you want to keep your changes or results.
00 — DROPPS 1.0 quickstart
Best for: first-time users who want one short, end-to-end demonstration.
Build a coarse-grained model, prepare a compact example simulation, run it, and inspect the generated files. Short demonstration settings keep the notebook practical for an initial Colab session.
01 — Model and system builder
Best for: constructing reproducible coarse-grained protein systems from sequence or structure information.
Configure the sequence, force field, termini and optional modifications;
generate molecular topology and coordinates; and insert many copies into a
compact cubic box. The default example uses 80 monomers of
FWFWFWFWFWFWFWFW.
02 — Phase-separation simulation
Best for: running the slab-protocol simulation used by the accompanying publication workflow.
Equilibrate the compact cubic system under NPT, expand only the z dimension by a fixed factor of 10, and continue in the elongated box under NVT. The Lennard-Jones and Coulomb cutoffs both default to 1.5 nm. The notebook preserves NPT and NVT outputs separately so downstream analysis can use only the NVT trajectory.
03 — Trajectory preparation
Best for: converting raw simulation output into consistent inputs for quantitative analysis and visualization.
Upload or reuse the elongated-box NVT results, inspect the trajectory, handle periodic boundaries, centre the condensate, and export a prepared trajectory together with matching structure and run-input files.
04 — Phase-separation analysis
Best for: extracting publication-oriented observables from the elongated NVT trajectory.
Calculate the density profile along z and save both density.xvg and
density_z.png. Optional analyses cover coexistence behaviour, molecular
contacts, radius of gyration and exchange dynamics. Every plotted analysis
is exported as a PNG file for inspection and reuse.
Reproducibility notes¶
The website copies are tied to the DROPPS 1.0 workflow. The notebooks install
the immutable v1.0.0 wheel from the official GitHub Release. Increase the
NPT and NVT step counts before using the workflow for production science; the
short defaults are intended for demonstration and validation.