GROMACS version: 2020.3
GROMACS modification: Yes
Hello Gromacs forum users, I am interested in using ‘gmx principal’ in my research, but currently I have trouble interpreting the output paxis1.xvg.
Based on the manual, the generated columns in the file are the time / x / y / z component of the first principal axis. But shouldn’t be the axis described by two points, not one point, since it is a line?
With the hope of getting a better understanding, I experimented with the following command: gmx principal -f prod.xtc -s prod.tpr -n index.ndx
where index.ndx is assigning only two indices.
index.ndx:
[ system ]
1, 2
My expectation was that Gromacs must give a warning or error saying that additional information (or coordinates) is required because at least 6 coordinates are required to determine the principal axes. However, Gromacs doesn’t generate any warning/error and generates non-zero values for the principal axes. It was puzzling to me and I still have no idea how to interpret the results. I would really appreciate it if someone had a better understanding of this function. Thank you so much!