Hi, I have a peptide sequence with 49 amino acids, which I want to show if it is acting as membrane protein using MD in membrane environment. We have experimental data showing that this peptide is localizing to ER membrane and TMHMM predicts TM domains. I used Robetta server to get a 3D structure prediction of the peptide and then used CHARMMGUI to build a membrane simulation. My question is what should I expect from MD simulations. What types of behaviors in ~200ns can support or disprove this peptide is a membrane protein. If you have any experience on this subject, any feedback and/or references are appreciated.

Thanks!