GROMACS version:2022.1
GROMACS modification: No
I have calculated moment of inertia (m.o.i) around each principal axes using gmx_principal. In the GROMACS manual it is written that first principal axis is the major axis and there are middle and minor axis next. What is the definition of major ,middle and minor axis here? Is it based on the highest or lowest value of m.o.i around a particular axis? or is it the standard Ixx, Iyy, Izz notation mapping to first (major), second(middle), third (minor) principal axis independent of the m.o.i. values?
I have calculated m.o.i. around each principal axis from the trajectory of a molecule in three different orientations ( Axes corresponding to Ixx , Iyy and Izz were pointed in Z direction for each orientation. Alignment was done using the orient program in vmd before running the system in GROMACS). Now I want to compare the values of Ixx, Iyy and Izz in three different orientation and hence, the confusion.
Any help regarding this matter will really be appreciated.