Analysis

MartiniGlass

MartiniGlass uses [vermouth] to stably rewrite your input topology files as ones that can be used for visualization in VMD. Although much of the functionality is focused on proteins, and the program has a particular focus on being able to visualize protein secondary/tertiary structure networks, MartiniGlass can in fact be used to reconstruct bonded networks of any Martini molecule!

Documentation for MartiniGlass is available on the [readthedocs] site. The documentation covers multiple use cases and runs through the tutorials in the [examples] folder step by step.

ProLint

Prolint2 is an optimized tool for analyzing and visualizing lipid-protein interactions from molecular dynamics trajectories at coarse-grained or atomistic resolution.

For more details and to download the latest version, visit the [GitHub repository].

MDVoxelSegmentation

When working with large systems containing multiple bilayers or other dynamic macroscopic objects, it tends to come more natural to give these aggregates an identity of their own. This is exactly what MDAVoxelSegmentation does for amphipathic Martini systems. It not only detects bilayers/leaflets or other aggregates using a voxel based architecture, but it also keeps track of such entities over time.

For more details and to download the latest version, visit the [GitHub repository].