[gmx-users] malloc on mac

[Justin A. Lemkul]

Sara baretller wrote:
> I have a question about the g-hbond selection . after i typed in the 
> g_hbond , it asked me to choose two groops and i am wondering what is 
> difference between Protein and Protein-H ?
> 

http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups

-Justin

> Thank you
> 
> Specify 2 groups to analyze:
> Group     0 (         System) has  7722 elements
> Group     1 (        Protein) has  2000 elements
> Group     2 (      Protein-H) has  2000 elements
> Group     3 (        C-alpha) has     0 elements
> Group     4 (       Backbone) has     0 elements
> Group     5 (      MainChain) has     0 elements
> Group     6 (   MainChain+Cb) has     0 elements
> Group     7 (    MainChain+H) has     0 elements
> Group     8 (      SideChain) has  2000 elements
> Group     9 (    SideChain-H) has  2000 elements
> Group    10 (    Prot-Masses) has  2000 elements
> Group    11 (    non-Protein) has  5722 elements
> Group    12 (          Other) has  5722 elements
> Group    13 (              W) has  5722 elemen
> 
> 
> 
> 
> On Thu, Jul 14, 2011 at 11:10 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> 
>     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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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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