[gmx-developers] Nr of graph edges per atom and distance restraints
hessb at mpip-mainz.mpg.de
Fri Mar 9 10:21:58 CET 2007
Juergen Haas wrote:
>On Thursday 08 March 2007 10:03, Berk Hess wrote:
>>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...
Line 166 is for the ensemble averaging code.
Are you really using ensemble averaging?
I don't see what could go wrong around that line.
The best thing would be to compile Gromacs with CFLAGS=-g
and run in the debugger.
>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
I don't undertand this last line.
How do you mean restraints originating from four atoms?
Orientations restraints only work on atom pairs.
And what do constraints have to do with orientation restraints?
>Since I have just started using restraints I might consider this a user
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