include NAMD dataset - Githubissues

alchemistry / alchemtest

the simple alchemistry test set

https://alchemtest.readthedocs.io

BSD 3-Clause "New" or "Revised" License

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include NAMD dataset #17

Closed orbeckst closed 6 years ago

orbeckst commented 6 years ago

Data set for a https://github.com/alchemistry/alchemlyb/issues/7 NAMD parser.

[x] add description in reST (include paper citation if appropriate)
[x] compress files
[x] add license (see contributing datasets)
[x] add entry to the reST files in the docs to reference the data set

orbeckst commented 6 years ago

@mrshirts @davidlmobley please sort out between your groups who wants to contribute test data. We can also include multiple datasets, we just need one to get started.

I had assigned @mrshirts based on today's discussion but obviously this is totally fluid. Just re-assign as necessary.

orbeckst commented 6 years ago

Potential NAMD FEP dataset:

@mrshirts: There's a data set from JC Gumbart for the Tyr->Ala example from the NAMD FEP tutorial that he gave me. The data files are at http://simbac.gatech.edu/forMichael/NAMD-FEP-tutorial-TYR2ALA.tgz — (https://github.com/alchemistry/alchemlyb/issues/7#issuecomment-347399820)
@vtlim: If this is the same Tyr->Ala example as in this tutorial, I've played around with some of their example output a while back. — (https://github.com/alchemistry/alchemlyb/issues/7#issuecomment-347410514)

orbeckst commented 6 years ago

@mrshirts @vtlim Have you been able to obtain permission from JC Gumbart to include NAMD FEP files under our terms for contributing data sets?

mrshirts commented 6 years ago

Yes, he has given permission for CC0.

orbeckst commented 6 years ago

Good news. Now, who is committing to adding the dataset? @mrshirts or @vtlim / @davidlmobley ?

vtlim commented 6 years ago

I can take care of it.

On Dec 7, 2017 at 09:35, <Oliver Beckstein (mailto:notifications@github.com)> wrote:

Good news. Now, who is committing to adding the dataset? @mrshirts (https://github.com/mrshirts) or @vtlim (https://github.com/vtlim) / @davidlmobley (https://github.com/davidlmobley) ?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub (https://github.com/alchemistry/alchemtest/issues/17#issuecomment-350039838), or mute the thread (https://github.com/notifications/unsubscribe-auth/AHY5nZTZKlpDzuRWNosOwk_OlwwNP9kfks5s-CHngaJpZM4Qsi5O).

orbeckst commented 6 years ago

@vtlim thanks, please assign yourself to the issue. I sent you an invite to join the project.