Lets suppose that I have an atom chain like system 1 below. Now, some interaction made one atom to move out of the chain, like shown in system 2 (the moved atom remains bounded but in another position). This change is permanent.

Knowing all the coordinates for all the atoms: Is it possible to define a property like strain to characterize the structural change?
(I'm not sure if the RMSD could be a good parameter to use here)

System 1: ************

System 2: ***** ******

1 Answer 1


I would select a group of atoms and calculate the relative deviation along the 3 dimensions. So I would take the initial (xi, yi, zi) and final (xf, yf, zf) coordinates and then calculate the 3N-dimensional distance using

$$\sqrt{(x_f-x_i)^2 + (y_f-y_i)^2 + (z_f-z_i)^2}$$

Those atoms there were not affected will have values zero, and values other than zero would reflect the extent change.

  • $\begingroup$ Assuming there is no uniform translation ... Depending on the method used you might have to correct for that. Similarly for rotations. $\endgroup$
    – Ian Bush
    Commented Oct 1, 2022 at 7:56

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