[gmx-users] g_disre problems

[Justin A. Lemkul]

Francisco Gomes Neto wrote:
>    Hello Everyone!
> 
>    I'm with  problems using g_disre where, after de execution, the answer is always
> "Segmentation fault". 
> 
>    To minimize the problem I changed for a very small system in the tutorial
> sub-directory of gromacs VERSION 4.5.4. I'm not using mpi library. 
>    
>    The distance restraints are:
> 
> [ distance_restraints ]
> ; ai    aj      type    index   type    low     up1     up2     fac
> 15      53      1       0       1       0.0     0.3     0.4     1.0
> 15      54      1       0       1       0.0     0.3     0.4     1.0
> 15      55      1       0       1       0.0     0.3     0.4     1.0
> 17      53      1       0       1       0.0     0.3     0.4     1.0
> 17      54      1       0       1       0.0     0.3     0.4     1.0
> 17      55      1       0       1       0.0     0.3     0.4     1.0
> 15      38      1       1       1       0.0     0.3     0.4     1.0
> 15      39      1       1       1       0.0     0.3     0.4     1.0
> 17      38      1       1       1       0.0     0.3     0.4     1.0
> 17      39      1       1       1       0.0     0.3     0.4     1.0
> 
> 
>  To analyse: 
>  g_disre -s topol.tpr -f traj.trr
> 
> and the answer is:
> 
> Back Off! I just backed up disres.log to ./#disres.log.2#
> Reading file ../topol.tpr, VERSION 4.5.4 (single precision)
> Reading file ../topol.tpr, VERSION 4.5.4 (single precision)
> Segmentation fault (core dumped)
> 
> in the file /var/log/messages
> 
> Aug  1 15:19:03 camboinhas kernel: g_disre[5743]: segfault at 4 ip 00007f71869e4222 sp
> 00007fff2970e170 error 4 in libgmx.so.6.0.0[7f7186987000+3b8000]
> Aug  1 15:19:03 camboinhas abrt[5744]: saved core dump of pid 5743
> (/usr/local/gromacs/bin/g_disre) to /var/spool/abrt/ccpp-1312222743-5743.new/coredump
> (622592 bytes)
> 
>     This results are the same in my MDs....
> 
>     I tried to recompile but the result is the same.
> 
>     Looking forward for your kind suggestions and comments
>  

This is a known bug in g_disre:

http://redmine.gromacs.org/issues/766

There is no fix yet.

-Justin

> Great Thanks
> 
>     Francisco
> 
> --
> ________________________________________________________ 
> Francisco Gomes Neto 
> Laboratório de RMN de biomoléculas (bioNMR) 
> Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas 
> Instituto de Bioquímica Médica 
> Universidade Federal do Rio de Janeiro 
> Av. Carlos Chagas Filho, 373, CCS, Bloco K, Anexo CNRMN 
> Rio de Janeiro, RJ, 21941-902 
> Phone: +55-21-3717-2019/3521-5558   Fax: +55-21-3881-4155 
> mobile:+55-21-9937-1621 
> fgomes at cnrmn.bioqmed.ufrj.br 
> http://cnrmn.bioqmed.ufrj.br
> 

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

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

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