[gmx-users] g_covar ends up complaining from a Segmentation Fault

[Justin A. Lemkul]

Peyman Yamin wrote:
> Hello everybody,
> 
> in an attempt to calculate the free-energy surface of a peptide, i
> followed exactly the procedure described in >> 
> http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA
>  <<< except that g_angle seems to need no -s option in my gromacs
> version(4.0.5).

You need the .tpr file for mass-weighting, I believe.

> Everything goes fine till the g_covar part where I get the
> Segmentation fault! I don't have the slightest idea what this error
> might want to convey!

Segmentation faults are general errors regarding memory allocation.  So no one 
here will have any idea what went wrong without seeing your command line, 
options chosen (if appropriate), etc.

-Justin

> I have had the seg. fault error previously, where I found out that it
> is caused by some miss-formatting in the files I edited manually. This
> time I edited nothing myself though and all files were made by GMX
> programs themselves!
> 
> Would be nice if I could get some comments, in case anyone has
> encountered this before.
> 
> Thanks in advance,
> greetings
> 
> Peyman
> 
> 
> -- 
> Peyman Yamin
> Computational Structural Biology Group
> Institut fuer Strukturbiologie und Biophysik (ISB)
> ISB-3: Strukturbiochemie
> Forschungszentrum Juelich
> D-52425 Juelich
> Tel:    (49)-2461-61-4230
> Fax:    (49)-2461-61-2023
> 
> 
> ------------------------------------------------------------------------------------------------ 
> 
> ------------------------------------------------------------------------------------------------ 
> 
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe
> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
> Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
> ------------------------------------------------------------------------------------------------ 
> 
> ------------------------------------------------------------------------------------------------ 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================