[gmx-users] malloc on mac

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 2 19:58:07 CEST 2011



Sara baretller wrote:
> 
> 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
> 
> 

If there are no hydrogens, there is nothing for g_hbond to measure.  You need an 
atomistic representation such that D-H-A angles and distances can be measured.

-Justin

> 
> On Tue, Aug 2, 2011 at 1:01 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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>
>         <mailto: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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> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
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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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