Hi all,

I'm having trouble coming up with a design for a 'stable' dihedral measurement along the principle orientation of a helical protein in a GROMACS topology. I will use this measurement as a collective variable for the rotation of a helical peptide during a meta-dynamics simulation. The difficulty is that the protein itself will not only rotate, but it will naturally adjust the atoms I assign as part of the CV, an consequently skew the dihedral measurements.  

The attached images should give an idea of what I am trying to design. I would like a 'ghost' virtual site (there are no interactions, no calculation) at right angle to the first C-alpha, which then connects to the second C-alpha, which is at right angle with the second 'ghost' virtual site. 

No matter what design I come up with, e.g., using 4 C-alpha and two C-beta atoms to design a virtual_site2, I always think this will fail. 

I thought perhaps a GHOST ATOM in PLUMED might help, but the documentation states: "Calculate the absolute position of a ghost atom with FIXED coordinates in the local reference frame formed by three atoms. The computed ghost atom is stored as a virtual atom that can be accessed in an atom list through the the label for the GHOST action that creates it." Thus it is FIXED. I would need the atom coordinates to adjust as PLUMED meta-dynamics encourages the simulation to explore phase space along the defined dihedral CV.

I wonder if anyone has any idea on the best approach. 

Many thanks

Anthony