Work

MartiniGlass: a Tool for Enabling Visualization of Coarse-Grained Martini Topologies

Year: 2025

Type: article

Abstract: As molecular modeling gains ever more prominence in understanding cellular processes, high quality visualization of models and dynamics has never been more important. Naturally, much molecular visualization software is written to enable the visualization of atomic level details in structures. While necessary, this means that visualization of increasingly popular coarse-grained (CG) models remains a challenge. Here, we present a Python package, MartiniGlass, that facilitates the visualization of systems simulated with the widely used CG Martini force field using the popular visualization package VMD. MartiniGlass rapidly processes molecular topologies and accounts for important topological features at CG resolution, such as secondary structure restraints, preparing them for easy visualization of simulated trajectories.

Source: Journal of Chemical Information and Modeling

DOI: 10.1021/acs.jcim.4c02277

Authors: Christopher Brasnett, Siewert J. Marrink

Institution: University of Groningen

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $4,500

Funder: Novo Nordisk Fonden