[gmx-users] angles without bonds - SegFault

Berk Hess gmx3 at hotmail.com
Fri Dec 3 11:13:56 CET 2004

>From: Marcin Wojdyr <wojdyr at unipress.waw.pl>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: [gmx-users] angles without bonds - SegFault
>Date: Thu, 2 Dec 2004 23:25:18 +0100 (CET)
>I tried to run simulation where the only bonded interactions are
>angles and noticed that mdrun segfaults.
>It can be reproduced with methanol tutorial. When I remove bonds
>from methanol.itp, it also segfaults. I tried to debug it, and
>it seems to me that the program tries to access graph->ishift[some_index],
>but graph is empty (graph structure is not filled when there are no bonds):
>(gdb) p *graph
>$3 = {maxedge = 6, nnodes = 0, nbound = 0, start = 648, end = 0, nedge = 
>   edge = 0x0, ishift = 0x0, negc = 0, egc = 0x0}
>Is this a bug or bonds are required by design?

This is by design.
We assume that all normal 'chemical' interations are only through bonded 
This saves some (but maybe a neglegible amount of) time in the code.
If you want angles without bonds you need to add the IF_GRAPH flag to 
in src/gmxlib/ifunc.c and recompile gromacs.


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