[gmx-users] segmentation fault in g_anaeig

Inon Sharony InonShar at post.TAU.ac.IL
Sun Aug 3 14:57:32 CEST 2008

 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): 


grompp_d em.mdp   ;energy minimization

mdrun_d em.mdp 

grompp_d nm.mdp  ;write Hessian matrix

mdrun_d nm.mdp 



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
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