[gmx-users] Segmentation fault

[David van der Spoel]

Ashutosh Jogalekar wrote:
> Well, the log file says that the protocol is dying even before it  
> starts the MD...so it stops right after it says
> 'Initializing LINear Constraint Solver'
> after which it displays the segmentation fault.
> Thanks

try running with the following:

setenv LOG_BUFS 0
mdrun -debug -v -nocompact

and see if you get information in either the md.log or the mdrun.log file.

> Ashutosh
> 
> On Mar 6, 2006, at 1:30 PM, Mark Abraham wrote:
> 
>> Ashutosh Jogalekar wrote:
>>
>>> Hello everyone
>>> I am doing MD on a peptide, and everything including the EM seems  
>>> to  go well. When I start to do the position restrained MD (or  even  
>>> directly the MD without doing the PR MD), I get a  "Segmentation  
>>> fault". I know that this is a generic error and  cannot point 
>>> directly  to a specific source for the problem; on  the other hand, 
>>> there must  be some specific source. So I was  wondering whether 
>>> anyone else has  fixed this problem in a  particular manner. I 
>>> checked my input and  everything seems to be  ok at first sight.
>>
>>
>> gromacs is normally quite graceful about dying and telling you  where 
>> it is dying, and sometimes why. You will need to provide the  last 
>> section of the .log file.
>>
>> Mark
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> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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