[gmx-users] malloc on mac

Itamar Kass itamar.kass at monash.edu
Fri Jul 15 03:48:10 CEST 2011

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 

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.

Thanks in advance for any idea,


"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut

| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at monash.edu

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