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kassonlab / gmxapi

(outdated) fork of https://gitlab.com/gromacs/gromacs
http://gmxapi.org/
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How to replace coordinates in the simulation input #271

Closed ghost closed 2 years ago

ghost commented 2 years ago

Hello,

I noticed that coordinates in the simulation input can be modified/replaced by using gmxapi.modify_input (https://gitlab.com/gromacs/gromacs/-/issues/3295). May I ask which parameter shoud be written in gmxapi.modify_input(input, parameters: [dict], label: Optional[[str]= None, context=None)？

Thank you very much!

eirrgang commented 2 years ago

Issue 3295 is under development this summer. I hope to have a complete solution in a month or two.

The "related branches" linked from that issue include some prototype / proof-of-concept work, but only expose a low-level interface (at the Python bindings). A high-level interface (gmxapi.modify_input()) is not yet available.

Please feel free to comment on #3295 so that the conversation is not spread across too many forums.

edit: If you would like to comment, but are unable to, please let me know. (You are welcome to contact me directly or by any means that is convenient to you, but I would like to encourage a clear and open conversation in a way that is most useful to the most people.)