<p> 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):</p>
<p>editconf_d <br /></p>
<p>grompp_d em.mdp ;energy minimization<br /></p>
<p>mdrun_d em.mdp</p>
<p>grompp_d nm.mdp ;write Hessian matrix<br /></p>
<p>mdrun_d nm.mdp</p>
<p>g_nmeig_d</p>
<p>g_anaeig_d</p>
<p><br /></p>
<p>when running this last command I got:</p>
<p><br /></p>
<p>trn version: GMX_trn_file (double precision)<br />Read mass weighted average/minimum structure with 5 atoms from eigenvec.trr<br />Segmentation fault<br /><br /></p>
<p>Why do I get a segmentation fault (segfault)? <br /></p>
<p>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?</p>
<p>I looked at the eigenfreq.xvg and saw 2 zero frequencies, and 4 more which are nearly zero.<br /></p>
<p>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)</p>
<p>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).</p>
<p><br /></p>
<p>Any and all assistance would be greatly appreciated. <br />Enjoy your weekend,<br /></p>
<p class="imp-signature"><!--begin_signature-->-- <br />Inon Sharony<br />ינון שרוני<br />+972(3)6407634<br />atto.TAU.ac.IL/~inonshar<br />Please consider your environmental responsibility before printing this e-mail.<!--end_signature--></p>