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

David van der Spoel spoel at xray.bmc.uu.se
Mon Mar 19 09:14:29 CET 2007

hessb at mpip-mainz.mpg.de wrote:
>> Juergen Haas wrote:
>>>> To get things right,
>>>> you are using only distance restraints, no orientation restraints
>>>> and you get a segfault around line 166 or orires.c, not disre.c ??
>>> in that case I forgot to switch off orires...:(
>>> to wrap it up: the segfault seems to have been linked to fftw commands
>>> and it
>>> turned out that I overlooked a trivial error: the lam/fftw environment
>>> on my
>>> newly installed machine was broken.
>>> Fixing that solved all problems and I could use the suggested hack of
>>> increasing g->maxedge.
>>> Thanks!
>>> Juergen
>> To finally fix the bugzilla 66, which number of did you use instead of 4
>> on line 229 of mshift.c?
> This is not relevant.
> The code is quite small and puts only the chemical bonds in the graph
> for interactions within three bonds.
> But one can define as many long-range distance restraints as one likes.
> Therefore there is not limit to the number of graph edges.
>> Alternatively, the condition & IF_CHEMBOND on line 201 could be replaced
>> by & IF_BOND
> This does not help.

I think it will because then distance restraints are included, now only 
true chemical bonds are, and then the number will be determined dynamically.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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