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: [EMAIL PROTECTED]
___________________________________________________________________________
___________________________________________________________________________
Shao Yue
Institue of Biomechanics and Biomedical Engineering
Department of Engineering Mechanics
Tsinghua University
P.R. China
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____________________________________________________________________________
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