[gmx-users] eigenvectors with nan values

Mark Abraham Mark.Abraham at anu.edu.au
Mon Aug 20 01:23:26 CEST 2012

On 20/08/2012 4:34 AM, Joaquim Rui de Castro Rodrigues wrote:
> Dear Gromacs users,
> I'm having problems with g_covar because sometimes it produces eigenvectors with nan values. This is related with a previous post (http://lists.gromacs.org/pipermail/gmx-users/2012-July/073492.html).
> I checked the integrity of my xtc and tpr/pdb input files, and everything seems fine, as the following works OK:
> echo System System | /usr/local/gromacs455/bin/g_covar455 -s mainchain_init.tpr -f mainchain_apo.xtc -o eigenvalues.xvg -v eigenvectors.trr -xpma covara.xpm -xpm covar.xpm -l covar.log
> but running g_covar with parts of the same trajectory gives eigenvectors with nan values:
> echo System System | /usr/local/gromacs455/bin/g_covar455 -s mainchain_init.tpr -f mainchain_apo.xtc -b 2000 -e 22000 -o eigenvalues_1.xvg -v eigenvectors_1.trr -xpma covara_1.xpm -xpm covar_1.xpm -l covar_1.log -av av_1.pdb -ascii covar_1.dat
> echo System System | /usr/local/gromacs455/bin/g_covar455 -s mainchain_init.tpr -f mainchain_apo.xtc -b 22000 -e 42000 -o eigenvalues_2.xvg -v eigenvectors_2.trr -xpma covara_2.xpm -xpm covar_2.xpm -l covar_2.log -av av_2.pdb -ascii covar_2.dat
> eigenvectors_1.trr has one frame with all coordinates set to nan; eigenvectors_2.trr has 17. I don't see anything obviously wrong with the other files produced (xvg, xpm, pdb).
> What could be the problem?

Not sure. Does the number of frames reported read by g_covar make sense? 
What's the frame frequency in your .xtc? What happens if you use trjconv 
to make the trajectory subsets before using g_covar without -b and -e? 
What's in System? Does double precision behave the same? Are the 
corresponding eigenvalues also nan?


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