[gmx-users] angles without bonds - SegFault

Marcin Wojdyr wojdyr at unipress.waw.pl
Fri Dec 3 15:39:25 CET 2004

On Fri, 3 Dec 2004, Berk Hess wrote:

> This is by design.
> We assume that all normal 'chemical' interations are only through bonded 
> atoms.
> 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 

Thanks, it seems to work (it starts simulation).

But the program still behaves differently when there are no bonds
and when there are zeroed bonds. Unfortunatelly I don't have any good 
topology for testing (I still have problems with my ZnS) so I tested it on 
methanol from tutorial with constraints=none. 

If bonds are set to zeros, mdrun just segfaults, but if there are no 
bonds, the output says it is an internal bug:

Step 2  Warning: pressure scaling more than 1%, mu: 179.299 179.299 179.299
Program mdrun, VERSION 3.2.90_beta_20040828
Source code file: nsgrid.c, line: 220
Fatal error:
Number of grid cells is zero. This should never happen, and
is either due to an internal Gromacs bug or a compiler error.

Is the second error caused only by unphysical forces and will it
work with well-constructed topology (without bonds)?  


Marcin Wojdyr                       http://www.unipress.waw.pl/~wojdyr/

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