Dear Alexander,

To follow up with our discussion:

I think the D2min and the MSD (once the affine displacements have been removed should be similar because we are actually talking about mean squared displacements in both situations. D2min takes the neighbouring stresses into account, which I considered kind of a "correction" to the MSD. That is why I wasnt expecting such differences. Once again, to get an average 1.2 A D2min (1.2 mean squared distance) in a solid system at room temperature after just 0.12 ps from the starting of the simulation sounds excesive to me, but I could also be totally wrong

The value of the D2min is the same with or without the option "detect reduced coordinates" as it should be. That was an error from my side.

I actually was going to make a post stating that the D2min value increases considerable with the length of the cutoff, but I didn't have the time and now it is no neccesary because you explanation covers it perfectly.

Now my question is: from a scientific point of view, shouldnt the D2min in the output be already normalized by the number of neighbours taken into account during the calculations? What do you think? I mean, I dont see an "average between neigbours" in the Falk and Langer paper, but I dont know, I wasnt expecting such big variations depending on the cutoff and my point is that the D2min should be more or less independent of the cutoff (from a logical minimum cutoff onwards). I would really appreciate your opinion on this one

On the other hand, I would really like to try and normalize the D2min with the number of neighbours taken into account. I appreciate that you explained me how to do it, but it is still not 100% clear to me. When you say "the number of neighbors in the reference configuration can be determined using the Coordination Analysis modifier and a Freeze Property modifier." I get confused. Do you mean that I should calculate once the number of neighbours for each atom inside the cutoff using the reference snapshot and then apply those numbers along the rest of the trajectory? From my point of view, the number of neighbours will change along the trajectory so I will need to recalculate them in each snapshot, right? I would also appreciate a lot some more insight on this issue.

In any case, thanks for your response and once again thanks for OVITO. I am getting the hang of it and it is really great!

Pablo.