[gmx-users] malloc on mac

[Sara baretller]

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 ?

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>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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