[gmx-users] seg fault with distance restraints - problem in graph

[David]

On Wed, 2004-02-25 at 22:38, Michael Shirts wrote:
> I'm playing around with the distance restraint options in gromacs-3.1.4,
> trying to get a better idea of what the results are.  I set up a model system
> with just two LJ atoms, but it keeps crashing.  Included are .top, .mdp, .gro,
> and .ndx. I debugged it, and it seems to be having problems setting up the
> bonded graph -- looking at the bonded graph, it looks like-
> 
> *g = {maxbond = 6, nnodes = 0, nbound = 0, start = 2, end = 0, nedge = 0x0,
> edge = 0x0, ishift = 0x0}
> 
> Which does not appear to be correct.
> 
> When mdrun reaches the line in function ta_disres
> 
>             ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
> 
> it gags, because g (the graph array) isn't set up correctly.
> 
> Any suggestions?  Am I doing something wrong to get distance restraints set
> up?
you can try adding a bond with zero force constant. or maybe upgrade to
3.2

> 
> Thanks,
> Michael Shirts
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
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