[gmx-developers] genbox EXC_BAD_ACCESS on OSX/Intel

[Charlie Peck]

I'm using a recent checkout of the .99 development branch on OSX/ 
Intel.  When I follow the demo tutorial instructions with genbox I  
get the following:

genbox -cp cpeptide.gro -cs -o cpeptide_b4em.gro -p cpeptide.top
...
Removed 2895 atoms that were outside the box
Bus error

gdb shows:

Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_PROTECTION_FAILURE at address: 0x000001d4
0x0001d7c1 in atoms2md (atoms=0x13028e0, ir=0x0, norires=0, nindex=0,  
index=0x0, md=0x1302a40) at mdatom.c:119
119         if (opts->ngtc > 1) {
(gdb) backtrace
#0  0x0001d7c1 in atoms2md (atoms=0x13028e0, ir=0x0, norires=0,  
nindex=0, index=0x0, md=0x1302a40) at mdatom.c:119
#1  0x00007163 in do_nsgrid (fp=0xa0001c18, bVerbose=1,  
box=0xbffff564, x=0x7d5000, atoms=0x13028e0, rlong=0.479999989) at  
addconf.c:241
#2  0x00007b4b in add_conf (atoms=0xbffff590, x=0xbffff58c, v=0x0,  
r=0xbffff60c, bSrenew=1, box=0xbffff564, bInsert=0,  
atoms_solvt=0x13027d0, x_solvt=0x7a1000, v_solvt=0x0,  
r_solvt=0x761000, bVerbose=1, rshell=0, max_sol=0) at addconf.c:370
#3  0x000041ab in add_solv (fn=0x1300420 "spc216.gro",  
atoms=0xbffff590, x=0xbffff58c, v=0x0, r=0xbffff60c, box=0xbffff564,  
atomprop=0x1300530, r_distance=0.104999997, atoms_added=0xbffff560,  
residues_added=0xbffff55c, rshell=0, max_sol=0) at gmx_genbox.c:420
#4  0x00005235 in gmx_genbox (argc=1, argv=0xbffff6cc) at  
gmx_genbox.c:740
#5  0x00001f66 in main (argc=8, argv=0xbffff6cc) at genbox.c:51

Is there something new about genbox that I need to learn?

thanks,
charlie