GROMACS version: 2020.4
GROMACS modification: No
performing duplicates of an md with the pull code to separate two proteins (in order to generate starting conformations for umbrella sampling), one of them sometimes remains in the starting conformation observed for the complex (from a CryoEM structure), but sometimes suffers a conformational change, elongating, while the other protein is being pulled away.
I would like to explore if these two different conformations for protein A are relevant or if I could dismiss the elongated one as an artifact of the pulled md (the other conformation is also observed in other unbound structures, it is assumed to be biologically relevant).
Is there a way to compare these two to determine if one of them is more unfavorable than the other one in terms of energy?