[gmx-users] segmentation fault with fitted gro files

[Marta Murcia]

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
Thanks so much
M