[gmx-users] Segmentation fault in g_hbond

[Erik Marklund]

Erik Marklund skrev 2010-12-18 16.23:
> leila karami skrev 2010-12-18 16.18:
>> Dear Erik
>>
>> excuse me, I sent .xtc and .tpr file your e-mail.
>>
>>
>>
>> -- 
>> Leila Karami
>> Ph.D. student of Physical Chemistry
>>
>> K.N. Toosi University of Technology
>> Theoretical Physical Chemistry Group
>>
> I can reproduce the segfault. It doesn't happen without -hbn. I'll 
> have a crack at fixing it. I won't promise to have it done before 
> christmas, but I'll try.
Fixed it. There's a call to clearPshift in do_merge which causes a 
segfault if g_hbond is run without -geminate. Here's what you do:

In gmx_hbond.c, enclose the call in an if-statement:

if (hb->per->pHist)
{
     clearPshift(&(hb->per->pHist[a1][a2]));
}

I'll push this to the master and release branches some time today.

Thanks for reporting this.

Regards,

Erik
>
> -- 
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> erikm at xray.bmc.uu.se     http://folding.bmc.uu.se/


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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