[gmx-users] malloc on mac

[Sara baretller]

does the g_hbond work for course grained file. i tried this command and it
gave me nothing but an error it does not matter wich selection



On Tue, Aug 2, 2011 at 1:01 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<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 <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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> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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