[gmx-users] negative eigenvalues occured and not "nearly zero"
gmx3 at hotmail.com
Fri Apr 25 11:53:23 CEST 2008
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"
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)
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
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.
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
I really need your help,
E-mail: silvester.thu at gmail.com
Institue of Biomechanics and Biomedical
Department of Engineering Mechanics
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