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

[Juergen Haas]

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 
anymore.
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 
atoms).

Since I have just started using restraints I might consider this a user 
problem:-)

regards

Juergen

-- 
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
 Germany