[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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