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Work around a GROMACS post-processing bug

Sebastian Wingbermuehle requested to merge fixPostProcessingBug into main
  • Adds a Python script that makes starting structures as .gro files whole
  • Integrates this Python script into tools/copy-convert.sh
  • Integrates this Python script into scripts/getFreeEnergies1.sh

The Python script has so far been tested on two systems only. Please test a bit more and let me know if you run into errors!

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