[gmx-users] what do negative eigenvalues imply?

[David van der Spoel]

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
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se