Hello Vitaly-- > > I am still confused how to use "create_PosDiffPot" if I want to move > parts of the structure as a rigid body during the calculation. For > instance in the attached script I was anticipating the peptide to get > superimposed onto the reference at the end of minimization routine, > which does not happen. >
PosDiffPot is an NCS type potential, so it actually does not try to overlay the atomic coordinate, but rather optimizes a rigid-body fit- so in a rigid body fit, its energy cannot change. The RMSD value reported for PosDiffPot should actually be the same as that reported by targetRMSD. Charles
