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

silvester.thu silvester.thu at gmail.com
Fri Apr 25 12:45:32 CEST 2008

Hi Berk, thanks for your reply, but there are still problems.

While the first six eigenvalues are corresponding to the three translational and three rotational dimensions of freedom of the whole system, they should be zero (theoretically) or at least not much different from zero (e.g: 1e-3 or -1e-3). But in my problem, I encountered some negative values that are much different from zero, as I listed before. 

And I have used the g_nmtraj_d to generate and visualize the modes corresponding to those negative eigenvalues, and I found that those modes were neither translational nor rotational movements -- they were actually "oscillational movements". It is unreasonable. So I guess there might be something wrong in my calculation. But, I still can not figure out what is wrong, even after I discussed with members in my group this morning.

Thanks for your attention!

With my best regards.

Yue Shao



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

发件人: Berk Hess
发送时间: 2008-04-25 17:54:51
收件人: Discussion list for GROMACS users
主题: RE: [gmx-users] negative eigenvalues occured and not "nearly zero"


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.


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

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 input files or give me some advice. If you need any more information, please e-mail me.

I really need your help, thanks.

Yours Sincerely

Yue Shao

E-mail: silvester.thu at gmail.com


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

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