AMBER Archive (2006)

Subject: AMBER: ptraj quasiharmonic analysis question

From: Shawn yy (
Date: Fri Aug 11 2006 - 09:45:21 CDT

I used 'analyze matrix' command of ptraj in AMBER 9 to calculate the modes
from a 4ns MD trajectory(4000 frames). But why the frequences of the first 6
modes are not zero? They are from 1.x to 3.x. Or the first 6 zero frequency
modes have been excluded in the output? Thank you very much for your help.

Shawn Yang

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