Create a folder with all scripts to reproduce the data in our paper - Githubissues

pyMBE-dev / pyMBE

pyMBE provides tools to facilitate building up molecules with complex architectures in the Molecular Dynamics software ESPResSo. For an up-to-date API documention please check our website:

https://pymbe-dev.github.io/pyMBE/pyMBE.html

GNU General Public License v3.0

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Create a folder with all scripts to reproduce the data in our paper #3

Closed pm-blanco closed 5 months ago

pm-blanco commented 6 months ago

Currently, there are some issues that we need to solve to make easy to reproduce the data from our paper:

The scripts used to produce the data in our paper are scattered between samples and tests
The scripts for peptides are case-specific #18
We need a "main" script capable to run "tests/simulation_script_grxmc.py" to reproduce the data in reference_data/data_landsgesell.csv @davidbbeyer

TODO:

[x] Move all scripts necessary to reproduce the data to a new folder /samples/Beyer2024
[x] Develop a script to reproduce the data in Beyer2024
[x] Adapt the script to reproduce the data in Fig. 6 of Beyer2024
[ ] Adapt the script to reproduce the data in Fig. 7 of Beyer2024
[ ] Adapt the script to reproduce the data in Fig. 8 of Beyer2024
[x] Add a Readme file explaining how to reproduce the data of our paper and with the citation.