[gmx-developers] Generalized Born - Crashes

David van der Spoel spoel at xray.bmc.uu.se
Sat Apr 11 23:45:34 CEST 2009


now I typed in some parameters, and EM works fine (apparently GB is not 
used there?), but MD crashes at step 0 due to memory allocation problems:
(gdb) up
#3  0x000000000049472c in init_gb (p_born=0x7fff0c32a160, cr=0x754c010,
     fr=0x759b820, ir=0x7759040, mtop=0x75990b0, x=0x7846880, rgbradii=5,
     gb_algorithm=0) at /home/spoel/GROMACS/head/gmx/src/mdlib/genborn.c:500
500		snew(fr->gblist.jjnr,nalloc*2);
(gdb) p nalloc
$1 = 674711745

Why does it need to allocate 6.7 million times 2 elements in the 
neighborlist? Is there an O(N^2) algorithm at play here?
I have 36735 CG atoms.

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

More information about the gromacs.org_gmx-developers mailing list