We use gas-phase MD to study model proteins that are expected to give different response to activation, monitor what experimental readout they would give and compare with ion mobility mass spectrometry (IM-MS) experiments. We still use natural as well as designer proteins with specific structural features to investigate specific structural dynamics happening during the IM-MS experiments. Secondly, we will simulate glycans and glycoproteins in solution and gas phase. Glycans are extremely flexible, making their structure impossible to determine with conventional X-ray or Cryo-EM. By combining IM-MS and MD, we hope to develop tools to increase the insights in glycan structure. This project is possible because of our recent efforts in using the Fast Multipole Method and Gromacs for achieving good performance in gas-phase MD (Persson2024). It allows for time and length scales that would otherwise be highly challenging if not impossible. A second advancement, is the development of a machine learning (ML) force field, allowing new force fields to be easily constructed, extended, and applied to arbitrary molecules (Takaba 2024).