Thanks, Tsjerk, you're absolutely right. I looked at the bugzilla
reports about g_anaeig. Bug 30 was already fixed on my version of the
source (pre-compilation) code. Bug 198 might be still relevant since
it's status is listed as NEW and it hasn't been resolved yet. The
bugzilla listing is as follows:
Bug 198:
(quote:)
I encountered a segmentation fault when running g_anaeig, and found
out that it occurred when reading the eigenvectors. Apparently,
someone reported a similar problem for GMX 3.3.1. However, I looked
for the differences between the versions in eigio.c, and found out
that the original 3.3.1 code worked fine for me (under the specified
platform at least).
The changes I introduced:diff eigio.c eigio.org.c
110,112c110,112
< /* eignr=NULL; */
< /* eigval=NULL; */
< /*eigvec=NULL; */
---
eignr=NULL; eigval=NULL; eigvec=NULL;
Best,
Ran.
(end quote)
I'm not sure I understand how to implement this change: Currently, in
the eigio.c file in my source code the three lines do appear. Should I
turn them into comment lines and re-compile?
For general reference, I'm running GROMACS 3.3.3 on an AMD 64-bit
quadrocore, running under Fedora 8 and using bash. Any further
relevant details will be given happily.
Thanks again,
Inon.
Quoting "Tsjerk Wassenaar" <[EMAIL PROTECTED]>:
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
×× ×× ×©×¨×× ×
+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
--
Inon Sharony
×× ×× ×©×¨×× ×
+972(3)6407634
atto.TAU.ac.IL/~inonshar
Please consider your environmental responsibility before printing
this e-mail.
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