GROMACS version: 2021.4
Hello,
I would like to convert the ascii-formatted gmx covar matrix into a normalized cross correlation matrix. For this, I would like to be sure about the order of elements provided in this file. In the manual, it was indicated that this ascii file contains the elements of the covar matrix in the x1x1, x1y1, x1z1, x1x2, … order (gmx covar — GROMACS 2021 documentation). If so, then, for a two amino acid system, would the covar elements be listed as in the following?
x1x1, x1y1, x1z1
x1x2, x1y2, x1z2
y1x1, y1y1, y1z1
y1x2, y1y2, y1z2
z1x1, z1y1, z1z1
z1x2, z1y2, z1z2
x2x1, x2y1, x2z1
x2x2, x2y2, x2z2
y2x1,y2y1, y2z1
y2x2, y2y2, y2z2
z2x1,z2y1, z2z1
z2x2, z2y2, z2z2
Thank you very much for the help!
Best wishes,
Busra