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Acellera / htmd

HTMD: Programming Environment for Molecular Discovery
https://software.acellera.com/docs/latest/htmd/index.html
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Structure and parmfile are reversed #967

Closed tonigi closed 2 years ago

tonigi commented 4 years ago

https://github.com/Acellera/htmd/blob/8277231c7f70ce990971fcdce1fcd28b0cf8b941/htmd/protocols/production_v6.py#L210

This is more of a cosmetic issue. Using protocols with Amber FF creates something like this:

parmfile                parameters
structure               structure.prmtop

It would seem more logical to switch the file names: since parmfile is the Amber keyword which enables the FF one would expect the .prmtop, while structure is ignored.

stefdoerr commented 4 years ago

wasn't this some limitation of GPUGRID? that the parameters had to be called liked that?

tonigi commented 4 years ago

No: the files had to exist, but the use in input was irrelevant.

tonigi commented 4 years ago

To be clear: for consistency, for amber builds I'm proposing to

  1. swap the two arguments - this should have no consequence.
  2. If possible, the "structure" statement can also be dropped, but this may need checking.
stefdoerr commented 2 years ago

I'll close this since it's more of an ACEMD3 issue and I don't believe we are willing to change the logic of this.