Published February 17, 2023 | Version 1.1
Journal article Open

Unbreaking assemblies in molecular simulations with periodic boundaries

Authors/Creators

  • 1. University of Helsinki
  • 2. University of Groningen

Description

This data set contains all examples shown in figure 2 of the associated manuscript. Every example contains the original GRO, XTC, TPR and a folder called `whole` which contains the whole.gro, whole.xtc and a README with the input parameters. For the Hii example there is also a segmentation folder which contains the output of the leaflet segmentation. Additionally the folders for generating the SI have been added in v1.1.

- dipeptides

- self-assembly

- inverted hexagonal

- large vesicle

- undulate membrane (SI)

- speed comparison (SI)

Notes

The code for mdvwhole can be installed with `pip install mdvwhole` (python >= 3.8). The code is available at `https://github.com/BartBruininks/mdvwhole`.

Files

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