[gmx-users] malloc on mac

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jul 15 05:10:33 CEST 2011

On 15/07/2011 11:48 AM, Itamar Kass wrote:
> Hi all,
> I am trying to find all possible h-bonds between chains in my complex. 
> I am using:
> g_hbond_d -f system_run1_MD050_fitbb.xtc -s system_for_EM.tpr -n 
> system.ndx -g system_run1_MD050_fitbb_Hbond_all.log -num 
> system_run1_MD050_fitbb_Hbnum_all.xvg -hbn 
> system_run1_MD050_fitbb.xtc_Hbond_all.ndx
> and after reading 100ns the system crash and report:
> Reading frame    1000 time 100000.000   g_hbond_d(42677) malloc: *** 
> error for object 0xd: pointer being reallocated was not allocated
> *** set a breakpoint in malloc_error_break to debug
> I am suing gromacs 4.0.7 (double precision) on mac (10.6.8), which I 
> compiled myself (not via fink). I also tried to compile it using 
> dmalloc without success.

Sounds like a bug. Try g_hbond from a more recent version of GROMACS.

BTW, you should only compile and use tools in double precision if that 
extra accuracy is what you actually need. Otherwise you're just running 
slower than you need to. All tools can read files written at either 


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