[gmx-users] malloc on mac
sarabiocomputation at gmail.com
Tue Aug 2 17:39:09 CEST 2011
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 ?
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_
>> 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
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