[gmx-users] segmentation fault in g_anaeig

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Aug 3 18:02:24 CEST 2008

Hi Inon,

Please be as complete as you can when posting questions. You've
omitted the (probably) most important piece of information: what
version are you using? (You might also want to include platform, OS,
compiler, etc.). Note that just a few days ago it was already reported
on this list that g_anaeig of version 3.3.3 gave a segfault.



On Sun, Aug 3, 2008 at 2:57 PM, Inon Sharony <InonShar at post.tau.ac.il> wrote:
>  I am preforming a normal mode analysis (NMA) in Pentane, using the
> following command sequence (all functions ending in *_d are so named because
> they were compiled in double-precision into a directory where the single
> precision-functions already existed):
> editconf_d
> grompp_d em.mdp   ;energy minimization
> mdrun_d em.mdp
> grompp_d nm.mdp  ;write Hessian matrix
> mdrun_d nm.mdp
> g_nmeig_d
> g_anaeig_d
> when running this last command I got:
> trn version: GMX_trn_file (double precision)
> Read mass weighted average/minimum structure with 5 atoms from eigenvec.trr
> Segmentation fault
> Why do I get a segmentation fault (segfault)?
> Could it be because the energy minimization only reached a maximal force of
> 1E-02 kJ / mole nm instead of the recommended 1E-05? Or is it some more
> serious problem?
> I looked at the eigenfreq.xvg and saw 2 zero frequencies, and 4 more which
> are nearly zero.
> I've already issued "make distclean" before the re-compilation in
> double-precision (see my
> http://www.gromacs.org/pipermail/gmx-users/2008-August/035535.html)
> Also, I viewed the eigenvec.tpr file and, indeed, the coordinates are in
> double-precision format (i.e., five significant digits to the right of the
> decimal point are non-zero).
> Any and all assistance would be greatly appreciated.
> Enjoy your weekend,
> --
> Inon   Sharony
> ינון     שרוני
> +972(3)6407634
> atto.TAU.ac.IL/~inonshar
> Please consider your environmental responsibility before printing this
> e-mail.
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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