VMD-L Mailing List

From: Cardenas Lizana, Paul Antonio (pacl3_at_gatech.edu)
Date: Sat Mar 18 2017 - 13:30:07 CDT

Dear VMD list,

I am calculating the moment of inertia of my protein using the "measure inertia" command and its results, that provide the eigenvectors (principal axes), does not match the one calculated from the Moment of Inertia Tensor (also given by the command) I used the command

set sel [atomselect top "protein"]
measure inertia $sel moments eigenvals

The Moment of Inertia Tensor is supposed to be a symmetric matrix but this command always gives a lower triangular matrix. Is it possible that the Iyx (product of inertia) is a non-zero number but the Ixy is zero?

I tested the command using a cubic and rectangular box containing just water. I calculated the eigenvalues from these two Lower matrices (cubic and rectangle) and their values are consistent with the values fom vmd command and they are also consistent with the theoretical value, but for all cases the eigenvectors are different (completely!)

(cubic) 100x100x100
vmd command 951535040 950283840 949322432
matlab 950236160 951141376 949763776
Theory 966405361 966511727 966705026

(rectangle) 100x50x50
vmd command 145265952 144902512 57354940
matlab 144945696 145222352 57355352
Theory 148166971 148138528 59235499

However, for my protein, the results are not consistent although they are in same order of magnitude.

Protein
vmd command 25108766 19768864 13066714
matlab 22230918 22610754 13102672

Has anyone had successfully used this command? May I be missing something?

Thanks