GROMACS modification: Yes/No
I used Charmm-gui to build my initial structure of complex micelle and protein and I downloaded charmm-gui files. But now, because I don’t have any .tpr file I don’t know how should I analyze?
CHARMM-GUI provides you all the inputs for running the simulations. The README tells you all the steps. There’s nothing to analyze until you’ve actually run the simulations, anyway :)