[WIP] Settings for Gromacs MD protocol #6
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Hello @hannahbaumann! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:
Comment last updated at 2024-09-04 14:51:20 UTC |
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hannahbaumann
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| by default set by the verlet-buffer-tolerance and | ||
| verlet-buffer-pressure-tolerance options and the value of rlist is ignored. |
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Is it worth setting rlist if we don't have these as options?
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May be useful for energy minimization?
| energygrps: str = "" | ||
| """ | ||
| Group(s) for which to write to write short-ranged non-bonded potential | ||
| energies to the energy file (not supported on GPUs) | ||
| """ |
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Because of the GPU limitation, I think it's ok here to just not have them? Unless you think there's a use for them.
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I think this could be useful for troubleshooting, e.g. to see whether interactions are excluded between certain groups or not (I've used this for SepTop). But maybe this doesn't need to be user interfacing?
Co-authored-by: Irfan Alibay <[email protected]>
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