Welcome to the documentation for MartiniGlass!
MartiniGlass is a Python library for aiding with the visualisation of simulations performed with the Martini coarse grained force field using VMD.
Molecular visualisation software packages are generally developed to assume atomistic detail in input structures. When it comes to showing coarse grained models, this means that features such as bonds between contiguous beads are missed, because the distance between them is much larger than at atomistic resolution. Rendering quality images of coarse grained models - including Martini - is therefore a challenge.
MartiniGlass helps users overcome this challenge by preprocessing systems to prepare a set of input files for VMD. The files prepared enable VMD to draw bonds between coarse grained beads and show continuous molecules, rather than leaving users to render complex systems are a series of overlapping spheres to try to render a similar effect. Furthermore, MartiniGlass helps users visualise additional aspects of their systems that are common in Martini models, such as elastic network bonds necessary for retaining secondary and tertiary structure at coarse grained resolution.
The usage section provides basic information about the package. There are details about how to install MartiniGlass, and a basic example of how to get started.
Note
This project is under active development.