[gmx-developers] Nr of graph edges per atom and distance restraints

Juergen Haas jhaas at gwdg.de
Thu Mar 8 17:16:07 CET 2007

On Thursday 08 March 2007 10:03, Berk Hess wrote:
> Hi,
> I assume this mail was meant for Bert de Groot, not the developers list?
> Anyhow, the problem you mention has not been fixed (yet).
> We should make the graph memory allocation fully dynamic.
> To run your simulation, you need to increase the number 4
> on line 229 of src/gmxlib/mshift.c. Currently the code
> only supports 4 restraints per atom.
I have slowly increased this value until I do not get this error message 
mdrun, however, segfaults around line 166.c in orires.c...

to explain the restraints I apply:
I am using restraints originating from four atoms. In each case there is one 
restraint for almost every bb-N-H, but never more than one..
which means on four atoms we have around 140 constraints arising from the 
restraints from this atom, as well as to this atom(+3, from the other 3 

Since I have just started using restraints I might consider this a user 



Juergen Haas, PhD
 Max-Planck-Institute for Biophysical Chemistry
 Theoretical and Computational Biophysics Department
 Am Fassberg 11
 D-37077 Goettingen
 Tel. +49-(0)-551-2012313

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