[gmx-users] segmentation fault with fitted gro files

[David van der Spoel]

Marta Murcia wrote:
> Hi again,
> sorry about that, what I meant is that before even doing grompp I am 
> taking snaphots that I oriented with respect a particular conformation 
> (with trajconv or vmd) so I use gro files for the afm pulling that 
> correspond to fitted structures instead of the raw files that would come 
> out just by cutting the trajectory (with these there is no seg. fault at 
> all)


ok, then you should be more specific on the error. What happens, when? 
Try running with -debug and check the mdrun.log file

> Thanks
> M
> 
> David van der Spoel wrote:
> 
>> Marta Murcia wrote:
>>
>>> Dear all,
>>> I am running a series of AFM simulations starting from different 
>>> conformations taken from a trajectory (gmx 3.3). Everything works 
>>> fine, but if I try to orient all the snapshots with respect to a 
>>> reference (based on the protein superimposition) I get segmentation 
>>> fault for all of them while doing mdrun, except for the one that I 
>>> used as template in the alignment. My feeling is that the box of 
>>> water molecules is not being well understand. I was using the same 
>>> topology files as before but this shouldn't affect (should be?). Do I 
>>> need to do pdb2gmx again for the individual gro files. Does it have 
>>> something to do with genbox? What is wrong?
>>> Guys I really appreciate your help, I don't know what to do but I'd 
>>> bet there is something really stupid I am missing
>>
>>
>> it's not clear what you are doing.  how can you "orient snapshots in 
>> mdrun"?
>>
>>> Thanks so much
>>> M
>>>
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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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