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Benchmark systems for membrane simulations #186

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ohsOllila opened this issue Apr 26, 2024 · 0 comments
Open

Benchmark systems for membrane simulations #186

ohsOllila opened this issue Apr 26, 2024 · 0 comments

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@ohsOllila
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I have been recently asked few times to suggest benchmarks for lipid force fields, most recently by @davidlmobley in here #175.

Answer would be that our quality evaluation metrics is defined in our recent publication (https://www.nature.com/articles/s41467-024-45189-z), and systems with experimental data and reference simulations can be identified from our ranking lists, available via different access options:
https://colab.research.google.com/github/NMRLipids/databank-template/blob/main/scripts/plotQuality.ipynb
https://lolicato-nmrlipids-gui-app-qa2ffe.streamlit.app/
https://github.com/NMRLipids/databank-template/blob/main/scripts/plotQuality.ipynb

However, it might take some time and effort to go through the ranking list to identify the best systems. Therefore, I think that it would be good to collect a list of systems to be simulated to benchmark quality of new force field parameters. Such list should be quite straightforward to generate using the available API tools. Also manual selection from the ranking list is not an impossible task, but if done, we should make the result available.

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