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

[David van der Spoel]

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.
________________________________________________________________________
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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