[gmx-users] segmentation fault with fitted gro files

Marta Murcia mam2070 at med.cornell.edu
Sat May 20 19:34:39 CEST 2006

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 

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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