# [gmx-users] negative eigenvalues occured and not "nearly zero"

Berk Hess gmx3 at hotmail.com
Fri Apr 25 11:53:23 CEST 2008

```Hi,

But the 6 negative eigenvalues just corresponds to the 3 translational and 3 rotational
degrees of freedom of the whole system, or not?
You can check this by looking at the eigenvectors with g_anaeig.

Berk

Date: Fri, 25 Apr 2008 13:55:08 +0800
From: silvester.thu at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] negative eigenvalues occured and not "nearly zero"

Hello gmx-users:

I'm recently using Normal Mode
Analysis(NMA) of GROMACS package to calculate the foundamental frequency of
graphite systems. But I got some results that are unexplainable, and I can not
continue my work now.

For all the examples below, I use the double
precision GROMACS functions: grompp_d, mdrun_d, and g_nmeig_d. For the EM part,
I used the conjugated-gradients algorism, and for the NMA part, I used
"nm" integrator and included the full precision structure file: em.trr into the
.tpr input file.

For the systems that I applied no
restraints, the first six eigenvalues should be zero, or at least
"nearly zero" if we considering the accuracy of numerical calculating. But
the typical first twelve eigenvalues I got have the values below:
(after EM, the Fmax<5e-4)

1
-0.37993
2
-0.335177
3
-0.206887
4
-0.111813
5
-0.0381566
6
-0.0211911
7
0.0189381
8
0.0370517
9
0.0385126
10
0.093188
11
0.132927
12
0.169143

the first eigenvalue has larger absolute
value than the 7th eigenvalue, which should not happen for an unrestrained
system. WHY the first six eigenvalues are not zero or nearly zero? I guess
there might by something wrong in my input files, but I can not figure out
where it is. By the way, the topology files and coordinate files are surely
correct.

Another problem is:
For the system that I applied restraints to, which removed the
translation and rotation about the center of mass, the eigenvalues should be all
positive. But I still found that negative values occured.

1
-0.135621
2
-0.0745555
3
-0.0390086
4
-0.0108285
5
0.0101438
6
0.0553579

7        0.146471

8        0.162898

9        0.344921

10        0.396553

11        0.486316

12        0.544625
WHY?

If anyone used the NMA of GROMACS before and got
correct output, it will be very helpful if you can send me your parameters or
e-mail me.

thanks.

Yours Sincerely

Yue Shao

E-mail: silvester.thu at gmail.com

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Shao Yue
Institue of Biomechanics and Biomedical
Engineering
Department of Engineering Mechanics
Tsinghua University
P.R. China

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