[gmx-users] g_covar eigenval.xvg

[Tom Rodgers]

Hi All

I have used g_covar to produce a covariance analysis of a trajectory file
and am unsure of the eigenvalues produced.

I expected the numbers to start small (first six almost zero) and increase
as when I used g_nmeig on the Hessian; however, I get the opposite:

# This file was created
# by the following command:
# g_covar_d -f md.trr -s md.tpr -av average.gro -last 50 -mwa
#
# g_covar_d is part of G R O M A C S:
#
# S  C  A  M  O  R  G
#
@    title "Eigenvalues of the covariance matrix"
@    xaxis  label "Eigenvector index"
@    yaxis  label "(u nm\S2\N)"
@TYPE xy
         1 414915
         2 7545.63
         3 708.598
         4 190.938
         5 104.664
         6 38.1187
         7 34.4296
         8 28.4192
         9 23.6477
        10 20.7779
        11 17.4987
        12 15.2986
        13 14.9555
        etc.

I selected 'not solvent' for both the calculation of the average and
the covariance, but the number of eigenvalues produced does not stop at
either 50 as I asked for, or after the number of atoms with out solvent. It
prints values all the way to the total number of atoms with values of
essentially zero after about the first 1000. The eigenvectors does stop at
50 though.

I have searched the archive and can't seem to find any information on this.
Does anyone have any experience with this problem? My only thought is
to rewrite the .trr and .tpr files with out the solvent and try again, if
this is possible?

Thanks for any help,

Tom

-----------------------------------------------------------------------------------------------------
Dr. T. L. Rodgers
Biophysical Sciences Institute
Durham University
South Road
Durham
DH1 3LE
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