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.
Cheers, Tsjerk On Sun, Aug 3, 2008 at 2:57 PM, Inon Sharony <[EMAIL PROTECTED]> 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. > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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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