Clarification for CONTACTMAP definition

[Domenico Marson]

Dear all,

I'm trying to reproduce (part of) the results from the paper 

Galdadas, I.; Carlino, L.; Ward, R. A.; Hughes, S. J.; Haider, S.; Gervasio, F. L. Structural Basis of the Effect of Activating Mutations on the EGF Receptor. Elife 2021, 10, e65824. https://doi.org/10.7554/elife.65824.

on NEST: Project ID: plumID:21.027 

(which in turn refers to  another paper for the definition of the CV2 and CV3, which are based on CMDIST). The ultimate goal is to the apply the same procedure to another, similar, system.

I'm struggling to understand how to determine the R_0 value in the RATIONAL switching function. As far as I understand from the paper and the plumed documentation, I should put here the value of the distance between the two atoms in the reference structure. I downloaded the archive with all the data from Project ID: plumID:21.027, and measuring the distances between the atoms reported in CONTACTMAP, either from the active or inactive reference .gro file, I can't find a single value that match the relative R_0 value. At most, R_0 values seems ~2*the_real_distance_between_the_atoms.

Moreover, the R_0 values in the cmap_*.dat files seems to be restricted to a pool of 4 possible values (1.024, 0.870, 0.526 and 0.698), which I found strange.

PS: it's not a problem of angstrom vs nm :-)

Could someone please clarify to me where I'm understanding something terribly wrong?

Thanks in advance,

have a wonderful day,

Domenico