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Notebook feedback | MO – Gromacs output file writing takes a long time In one case, there were several molecules all grouped into (chain A, residue 150), and this messed up the output PDB, and the output prmtops. I made an openff top from the omm top from modeller, but then I wasn’t sure if this was somehow tainted by the use of modeller, so I wrote it out to pdb file, then I made an openff topology using from_molecules(water * n_waters...).
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