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Martinize2 tutorials#635

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pckroon merged 35 commits intomastermarrink-lab/vermouth-martinize:masterfrom martinize2_tutorialsmarrink-lab/vermouth-martinize:martinize2_tutorialsCopy head branch name to clipboardNov 19, 2024

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Commits

Commits on Oct 9, 2024

• first draft of martinize2 command tutorials

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• Merge branch 'master' into martinize2_tutorials

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• first draft of martinize2 command tutorials

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• Merge remote-tracking branch 'origin/martinize2_tutorials' into martinize2_tutorials

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• Merge remote-tracking branch 'origin/martinize2_tutorials' into martinize2_tutorials

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• Merge remote-tracking branch 'origin/martinize2_tutorials' into martinize2_tutorials

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• update index

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• refactor

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• refactor

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• Merge remote-tracking branch 'origin/martinize2_tutorials' into martinize2_tutorials

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• missed item in index

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Commits on Oct 10, 2024

• fixed equation formatting, added more -ss description

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• added note about polyply

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• corrected lines in go_models.rst for including go files in martini_v3.0.0.itp

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Commits on Oct 14, 2024

• Made requested changes

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• Update doc/source/tutorials/elastic_networks.rst

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• think there needs to be a blank line in the math to make it math

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Commits on Oct 21, 2024

• made requested changes

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• added missing overbars

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• update information about scfix and elastic network defaults.

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Commits on Oct 24, 2024

• Merge branch 'marrink-lab:master' into martinize2_tutorials

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• (hopefully) fix the relative links, add some small clarifications

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• (hopefully) fix the relative links, add some small clarifications

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• change rst to html

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• Merge remote-tracking branch 'origin/martinize2_tutorials' into martinize2_tutorials

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Commits on Oct 29, 2024

• Fix links to network pages

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• maybe this fixes the links

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• add refs

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Commits on Oct 30, 2024

• try doc referencing as per https://www.sphinx-doc.org/en/master/usage/referencing.html#cross-referencing-documents

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• Merge branch 'marrink-lab:master' into martinize2_tutorials

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Commits on Nov 13, 2024

• Merge branch 'marrink-lab:master' into martinize2_tutorials

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Commits on Nov 15, 2024

• Merge branch 'master' into martinize2_tutorials

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Commits on Nov 18, 2024

• Merge branch 'master' into martinize2_tutorials

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• add some information about the -name flag

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• nit

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