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
×× ×× ×©×¨×× ×
+972(3)6407634
atto.TAU.ac.IL/~inonshar
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