Re: [AMBER] Quasi harmonic bad eigenvalue error

From: Jason Swails <>
Date: Sat, 20 Jun 2015 12:33:36 -0400

On Sat, Jun 20, 2015 at 10:28 AM, D.J. Pattinson <> wrote:

> Dear Amber Users
> I’d like to use quasi-harmonic entropy approximation in MMPBSA
> calculations.
> I’m getting an error which I don’t know how to troubleshoot:
> Beginning quasi-harmonic calculations with
> /Users/david/bin/amber14/bin/cpptraj
> Error: DataSet_Modes: bad eigenvalue 0 = 0.000000
> Error: in Analysis # 0

​The quasi-harmonic approximation is based on the assumption that normal
modes can be approximated as mass-weighted covariance eigenvectors
(essentially a sort of mass-weighted principal component analysis). You
submitted only a single frame to You can't compute a covariance
from a single frame. In general, the covariance matrix will have only as
many non-zero eigenvalues as there are frames in the trajectory, I
believe. And you need many more frames in order to converge a
quasi-harmonic entropy approximation than you have atoms in your system.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sat Jun 20 2015 - 10:00:03 PDT
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