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

[Berk Hess]

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 
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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