ions.mdp missing about protocaller HOT 2 CLOSED

Hi @niko97320 ,

Thanks for the report. It turns out that the issue is due to GROMACS 2020 no longer supporting group neighbourlists. This is not a problem for genion, and I fixed it now but it does make me wonder whether running simulations in vacuum without periodic boundary conditions is no longer possible in GROMACS 2020? Because Verlet neighbourlists need periodic boundary conditions even in GROMACS 2020.

You can update ProtoCaller now. I am currently pushing the latest development versions to the main Conda channel, since the Protein Data Bank had a recent overhaul and and some of the functionality was broken and I will be relying on "nightly" builds until they fix that. You can always access older versions from the protocaller/label/dev channel, if you need to. For most cases it should be fine, though.

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Hi @niko97320

Thank you for letting us know about this, and we will work on it.

Meantime you can use GROMACS 2019.1 for your testing.
I see you are running ProtoCaller in a conda environment. So just install conda version of GROMACS into your conda env
conda install -c bioconda -c conda-forge gromacs=2019.1

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