GROMACS tutorial: Density fit simulations

Here, we use the GROMACS to perform density-fit (or density-guided) simulations. In density-guided simulations, additional forces are applied to atoms that depend on the gradient of similarity between a simulated density and a reference density. By applying these forces protein structures can be "fitted" to densities coming from, e.g., cryo electron-microscopy. The implemented approach extends the ones described in Orzechowski et al. and Igaev et al. More on the density guided approach implemented in GROMACS and a recently developed tool within GROMACS that can fit structures via Bayes' approach can be found in [Blau et al. bioRxiv 2022].