setup.py:energy_minimize ignores mdp parameter

[Luan Carvalho Martins]

In setup.py, line 662:

mdp = deffnm+'.mdp'

This overwrites user-supplied mdp parameter.

[Oliver Beckstein]

Yes – if you want to provide a PR I am happy to merge it. I won't be able to work on it during this week.

Thanks for reporting!

[Luan Carvalho Martins]

I can do so, but only between Friday and Sunday. Would you rather prefer setup.py:energy_minimize to try to alter user-supplied mdp file through cbook.py:editmdp or to use it as is? I tend to think that the former allows more flexibility.

You are welcome.

[Oliver Beckstein]

I would 'use as is'. Whenever you submit a PR is fine. It's open source, you contribute when you can. (And you will be listed as an author of GW).

…

-- Oliver Beckstein email: [e-mail]

Am Jun 27, 2017 um 13:24 schrieb luancarvalhomartins ***@***.***>: I can do so, but only Friday to Sunday. Would you rather prefer setup.py:energy_minimize to try to alter user-supplied mdp file through cbook.py:editmdp or to use it as is? I tend to think that the former allows more flexibility. You are welcome. — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[Oliver Beckstein]

I understood this issue that a user-supplied mdp parameter in function gromacs.setup.energy_minimize(mdp="custom.mdp") is ignored. In fact, this is not true and it works just fine with a supplied mdp file. The code is not very clear because the variable mdp changes meaning half-way through (sorry). I added a comment to the code and a test for a custom mdp file in PR #128.

(It is true that a custom em/em.mdp file would be overwritten and this is not checked for.)