[gmx-developers] Implicit solvent + Still radii + sse2_double = segmentation fault

Julius Su jsu at caltech.edu
Wed Nov 2 05:41:08 CET 2011

Hi everyone,

I observed segmentation fault errors in Gromacs 4.5.5 when the following 
options are enabled:

implicit_solvent = GBSA
gb_algorithm = Still

and additionally the sse2_double optimized kernel 
(src/mdlib/genborn_sse2_double.c) is used.

After some investigation, I believe that line 1199 of 
src/mdlib/genborn.c should be changed from
      calc_gb_rad_still_sse2_double(cr,fr,md->nr,top, atype, x[0], nl, 
     calc_gb_rad_still_sse2_double(cr,fr,born->nr,top, atype, x[0], nl, 
so that the correct number of atoms is passed to the Born radius function.

This eliminates the segmentation fault and enables the program to 
function properly.


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