it's possible that you are creating an array that is too large
somewhere, such as the exclusion list which will be huge in this case.
it may not be very efficient- for example, each of your 8596*30 atoms
will have 8596*29 atoms in the exclusion list using LES NEB,
8596*30*8596*29=64 million excluded atoms. you might try making things
smaller (fewer neb beads) and see if it helps. I'm not sure if anyone
has tried a system this large using LES NEB.
> Dear Amber users
> I am trying to do some nudged elastic banding simulation on a big protein (548 residues).
> I just went through this by reading the NEB tutorial, which is quite informative and helpful.
> (Many thanks to Dr. Ross Walker)
> However, when I used addles to create 30 copies of my protein. The output file said
> Checking topology sizes against compiled limits
> exceeded MAXANG in SIZE.BLOCK.
> MAXANG = 8000
> ntheth = 9788
> exceeded MAXDIH in SIZE.BLOCK.
> MAXDIH = 15000
> nphih = 18572
> Change SIZE.BLOCK and recompile.
>
> I searched the mailing list and found the SIZE.h file and increased these values to 10000 and 20000 respectively to fit my protein.
>
> after make clean,
> and make in the $AMBERHOME/src/addles/ folder
> I created a new addles program in this folder.
>
>
> But when I used this command in this folder to create the prmtop and inpcrd file.
> There came a segmentation fault
>
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
> addles 08051E1A Unknown Unknown Unknown
> addles 0804CD72 Unknown Unknown Unknown
> addles 08049B95 Unknown Unknown Unknown
> libc.so.6 0076EE33 Unknown Unknown Unknown
> addles 08049AD1 Unknown Unknown Unknown
>
> The input and output files are attached.
>
> I really don't know the reason for this.
>
>
> Please give some suggestions.
>
>
> Best Regards!
>
> Xiaonan Zhang
>
> Shanghai Public Health Clinical Center
>
>
>
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>
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Received on Wed Mar 11 2009 - 01:09:04 PDT
