CALVADOS: Coarse-graining Approach to Liquid-liquid phase separation Via an Automated Data-driven Optimisation Scheme

This repository contains Python code to run coarse-grained molecular dynamics simulations of intrinsically disordered proteins (IDPs) using the CALVADOS model.

Layout

• single_chain/: Python code to run single-chain simulations of IDPs using the CALVADOS model. python submit.py submits a simulation of a single ACTR chain on a single CPU.
• direct_coexistence/: Python code to run multi-chain simulations of IDPs using the CALVADOS model in slab geometry. python submit.py submits a direct-coexistence simulation of 100 A1 LCD chains on a single GPU.

In the examples, direct-coexistence and single-chain simulations are performed using openMM and HOOMD-blue installed with mphowardlab/azplugins, respectively.

This repository is also available at github.com/KULL-Centre/CALVADOS.

Usage

To run the code, install Miniconda and make sure all required packages are installed by issuing the following terminal commands

conda env create -f environment.yml
source activate calvados

References

G. Tesei, T. K. Schulze, R. Crehuet, and K. Lindorff-Larsen. PNAS 118(44), 2021. DOI: 10.1073/pnas.2111696118

G. Tesei and K. Lindorff-Larsen. Open Res Europe 2:94, 2022. DOI: 10.12688/openreseurope.14967.1