[gmx-users] segmentation fault with fitted gro files

David van der Spoel spoel at xray.bmc.uu.se
Sat May 20 09:49:11 CEST 2006

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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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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