[gmx-users] g_covar & g_anaeig problems

Arne.Wagner at student.uib.no Arne.Wagner at student.uib.no
Thu Mar 25 10:05:59 CET 2010

Hi everyone,
I've got the following two problems - hopefully someone can help me
fixing them.
I have a larger system ~20000 atoms where I performed an MD run and
now I want to analyze the entropy. I tried a combination of g_covar
and g_anaeig to get the values.
g_covar -f XXX_md_eq.xtc -n XXX.ndx -s XXX_md_eq.tpr -v XXX_eivec.trr
-mwa -l XXX_covar.log

If I choose a larger sub-part of the system (approx. > 4000 elements)
I get the following error message after the average structure is

Constructing covariance matrix ...
Reading frame       0 time    0.000   Segmentation fault

Is this a result of insufficient memory or is there an error in the
whole procedure?

In smaller sub-parts I can get the eigenvectors and when I put them
into g_anaeig,

g_anaeig -v XXX.trr -entropy

I get values for the quasi-harmonical-approximation but
an 'inf' oder 'nan' for the Schlitter entropy calculation - even with
additional/maximum input. Why?

Thanks a lot!

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