I'm interested in applying RMSD constraints to a pose using pyrosetta.
I currenly have a native pose which is deformed manually, such the the backbone RMSD with respect to the native is 1 Angstroms.
pose.residue(r).set_xyz(a, py.rosetta.numeric.xyzVector_double_t(new_coords, new_coords, new_coords))
However, when I relax (cartesian), I notice the structure relaxing back to the native, ie the RMSD decreases to ~0 Angstroms.
Im keen to apply constraints on the deformed coordinates before relaxing such that the RMSD of 1 Angstroms is maintained.
Currently, I have been applying coordinate constraints on the backbone of the deformed structure using a harmonic potential with a std dev of 0.5 Angstroms. But this is not ideal, as the backbone RMSD can still change.
There are parallels to this, for example using PLUMED for molecular dynamics simulations. I wish to know if I can implement this somehow in Rosetta? I would be really grateful to any insights. Feel free to contact me for any details/data.
Is there a general solution to the application of constraints to much more complex collective variables (CVs) in Rosetta?