Chris Neale wrote:
Hello,
I was wondering if anybody can explain why eigenvalues can be negative?
I have found a suggestion on the internet that this is because the
positive eigenvalues have accounted for more than 100% of the motion.
Does this sound accurate?
No
You normally have six negative eigevalues due to the fact that overall
translation and rotation are removed. You have in addition 4 that are
very small, maybe you can investigate how many degrees of freedom you
have (it says in the md.log file). This should be equal to the umber of
non-negative ev.
This system is the alanine dipeptide. I do not find such negative values
when running g_covar on full proteins.
The contents of eigenval.xvg are listed below.
# This file was created Mon Oct 29 16:31:46 2007
# by the following command:
# /hpf/data/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin/g_covar
-s ../adp.tpr -n ../adp.ndx -f ../adp_0-1.56us.xtc -ascii covar.dat -mwa
#
# /hpf/data/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin/g_covar
is part of G R O M A C S:
#
# Great Red Owns Many ACres of Sand
#
@ title "Eigenvalues of the covariance matrix"
@ xaxis label "Eigenvector index"
@ yaxis label "(u nm\S2\N)"
@TYPE xy
1 0.211327
2 0.0736961
3 0.0522046
4 0.04409
5 0.0104057
6 0.00577603
7 0.00198832
8 0.00163465
9 0.00128302
10 0.000735383
11 0.000649576
12 0.000434795
13 0.000376401
14 0.000337852
15 0.000191994
16 0.000131498
17 8.87514e-05
18 7.31975e-05
19 5.31939e-05
20 4.45637e-05
21 -5.03112e-06
22 -1.26812e-05
23 -2.48763e-05
24 -5.90268e-05
25 -0.000114215
26 -0.000227912
27 -0.000355243
28 -0.000513052
29 -0.000631471
30 -0.00178302
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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