I have a modeled protein 3D structure with tow cofactors.When i do molecular dynamics simulation whit gromacs, distances between them increase up to 9 A .while their distances after homology modeling was 3A. i freezed 2 cofactors and 1 aminoacid white freezegrps in .mdp file.Now their distances are normal and ok, but now potential energy of molecule is a positive number instead of being a minus one. any suggestion? it is a terrible problem. pleas help me.