I am studying membrane protein. I did an MD simulation using Desmond. My question is, what would be the maximum value of the C-alpha RMSD for the membrane protein?
The maximum value of the C-alpha RMSD (root-mean-square deviation) for a membrane protein cannot be determined without specific information about the protein and the simulation conditions. The RMSD is a measure of the average deviation of the protein's atoms from their positions in a reference structure, so the maximum value will depend on the reference structure used, the length of the simulation, and other factors. In general, longer simulations and more flexible proteins are likely to result in higher RMSD values.