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
precision.
Mark
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