Martignac: Computational workflows for reproducible, traceable, and composable coarse-grained Martini simulations

TL;DR

Martignac introduces a workflow framework for coarse-grained Martini MD simulations that enhances reproducibility, traceability, and data management by integrating with the NOMAD database and representing simulations as directed graphs.

Contribution

It presents a novel computational workflow system for Martini simulations that ensures reproducibility and traceability, connecting to NOMAD for data management.

Findings

Workflow representation as directed acyclic graph

Integration with NOMAD for data normalization and storage

Prototypical workflows for liquids, bilayers, and free-energy calculations

Abstract

Despite their wide use and far-reaching implications, molecular dynamics (MD) simulations suffer from a lack of both traceability and reproducibility. We introduce Martignac: computational workflows for the coarse-grained (CG) Martini force field. Martignac describes Martini CG MD simulations as an acyclic directed graph, providing the entire history of a simulation -- from system preparation to property calculations. Martignac connects to NOMAD, such that all simulation data generated are automatically normalized and stored according to the FAIR principles. We present several prototypical Martini workflows, including system generation of simple liquids and bilayers, as well as free-energy calculations for solute solvation in homogeneous liquids and drug permeation in lipid bilayers. By connecting to the NOMAD database to automatically pull existing simulations and push any new simulation generated, Martignac contributes to improving the sustainability and reproducibility of molecular simulations.