include Gromacs extended ensemble data set

[orbeckst]

To test extended ensembles produced with Gromacs we need to include a data set. alchemistry/alchemlyb#14 includes a zip file (provided by @mrshirts ) that need to be analyzed, evaluated if it fits into alchemtest, and eventually included.

[orbeckst]

@davidlmobley can you please add @trje3733 to the alchemistry org so that we can assign this issue to him? Thanks!

[davidlmobley]

Done. But, I also have you set as an administrator for alchemlyb and alchemtest so you should be able to add people to those directly via their settings without involving me.

[orbeckst]

Thanks!

On Nov 14, 2017, at 1:32 PM, David L. Mobley notifications@github.com wrote:

Done. But, I also have you set as an administrator for alchemlyb and alchemtest so you should be able to add people to those directly via their settings without involving me.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/alchemistry/alchemtest/issues/4#issuecomment-344389007, or mute the thread https://github.com/notifications/unsubscribe-auth/AAOhnDNYL33No1G45LZaCb_kmpK1StK7ks5s2fjygaJpZM4P_47F.

-- Oliver Beckstein orbeckst@gmail.com * orbeckst@gmx.net

[mrshirts]

We are developing 4-5 tests that handle different possible cases. Should each of these tests each be it's own directory, or be subdirectories of a single one? With only one example so far, it's hard to see what the directory structure should be.

[orbeckst]

The directory structure is flexible. The main thing is to make sure that you define good accessor functions.

Because it is Gromacs it should go under gmx and I would do something like

   gmx/
           benzene/             already there, simple TI and (M)BAR
           extended/            or whatever you deem a good name
                  case_1/
                  case_2/         ... 

In gmx/access.py I would add a accessor functions such as load_extended_case_1() etc. (We could modularize more but this might become overkill.)

Or do you think it will work better in some other way?

[orbeckst]

Btw, the amber test files now follow a similar pattern, see https://github.com/alchemistry/alchemtest/tree/master/src/alchemtest/amber

[trje3733]

Have I been added to alchemtest yet? If not, could I be added soon?

[orbeckst]

@trje3733 I thought you had been added to the org but I didn't see you there so I sent you invites as "collaborator" for alchemlyb and alchemtest. Let me know if they got stuck somewhere.

[orbeckst]

@trje3733 , for the development process see https://github.com/alchemistry/alchemlyb/wiki/Developer-Guide and create a PR. Thanks!