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

Berk Hess gmx3 at hotmail.com
Thu Feb 26 12:36:01 CET 2004


> > 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

This is a problem that has been fixed in 3.2.
In older versions there is this problem with distance restraints between 
unconnected atoms,
we simply did not think of this type of systems.
But adding a normal bond with zero force constant should also work.

Berk.

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