[gmx-users] g_rdf on Mac OS X 10.3, 10.4

[Kay Gottschalk]

I think we somehow fixed it in the attached version based on some  
advise we found in the user list, but can't really remember the  
change we made. Bad documentation. Try it out and see if it works.
Good luck,
Kay.


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On May 4, 2006, at 9:50 PM, David van der Spoel wrote:

> Jennifer Rendell wrote:
>> Dear friends,
>> I have seen a couple of postings (January 2004, gmx-developers,  
>> David Bostick, and November 2003, gmx-users, Kay Gottschalk) on  
>> segmentation faults from g_rdf on Mac OS X systems.
>> I am using the "Getting Started" section of the  gromacs web  
>> pages, in particular, the section on water, where the command  
>> g_rdf is called.
>> Below I show the results from two versions of gromacs, 3.2.1 on a  
>> Mac OS X 10.4, and 3.1.5_pre2 on a Mac OS X 10.3. The results are  
>> similar in that each results in a segmentation fault. g_rms and  
>> gmxcheck work as I expect.
>> Any ideas on how to fix this? Jennifer
>
> Maybe you don't want to hear this, but please upgrade to 3.3.1 and  
> try again. If the problem persists in the latest version please  
> post a bugzilla.
>
>
>> ********************************************************************* 
>> ********** 1. gromacs 3.2.1 on Mac OS X 10.4 (Tiger). g_rdf gives  
>> the following
>>    results:
>> % g_rdf -f water.trr -n oxygen.ndx -o rdf.xvg -s water.tpr
>>                          :-)  G  R  O  M  A  C  S  (-:
>>                Giving Russians Opium May Alter Current Situation
>>                             :-)  VERSION 3.2.1  (-:
>> (deleted some lines)
>>                                 :-)  g_rdf  (-:
>> Option     Filename  Type         Description
>> ------------------------------------------------------------
>>   -f      water.trr  Input        Generic trajectory: xtc trr trj  
>> gro g96 pdb
>>   -s      water.tpr  Input, Opt!  Structure+mass(db): tpr tpb tpa  
>> gro g96 pdb
>>                                    xml
>>   -n     oxygen.ndx  Input, Opt!  Index file
>>   -o        rdf.xvg  Output, Opt! xvgr/xmgr file
>> (deleted all remaining option lines)
>> Reading file water.tpr, VERSION 3.2.1 (single precision)
>> Reading file water.tpr, VERSION 3.2.1 (single precision)
>> How many groups do you want to calculate the RDF of?
>> 1
>> Select a reference group and 1 group
>> Group     0 (          OW) has   216 elements
>> There is one group in the index
>> There is one group in the index
>> trn version: GMX_trn_file (single precision)
>> Last frame         10 time   10.000
>> Segmentation fault
>> ********************************************************************* 
>> ********** 2. gromacs 3.1.5_pre2 on Mac OS X 10.3 (Panther). g_rdf  
>> gives the
>>    following results (which appear to be the same as the above):
>> $ g_rdf -f water.trr -n oxygen.ndx -o rdf.xvg -s water.tpr
>>                          :-)  G  R  O  M  A  C  S  (-:
>>                Go Rough, Oppose Many Angry Chinese Serial killers
>>                           :-)  VERSION 3.1.5_pre2  (-:
>> (deleted some lines)
>>                                 :-)  g_rdf  (-:
>> Option     Filename  Type          Description
>> ------------------------------------------------------------
>>   -f      water.trr  Input         Generic trajectory: xtc trr trj  
>> gro g96 pdb
>>   -s      water.tpr  Input, Opt!   Structure+mass(db): tpr tpb tpa  
>> gro g96 pdb
>>   -n     oxygen.ndx  Input, Opt!   Index file
>> (deleted all remaining option lines)
>> Reading file water.tpr, VERSION 3.1.5_pre2 (single precision)
>> Reading file water.tpr, VERSION 3.1.5_pre2 (single precision)
>> How many groups do you want to calculate the RDF of?
>> 1
>> Select a reference group and 1 group
>> Group     0 (          OW) has   216 elements
>> There is one group in the index
>> There is one group in the index
>> trn version: GMX_trn_file
>> Last frame         10 time   10.000
>> Segmentation fault
>> ********************************************************************* 
>> ********** _______________________________________________
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>
>
> -- 
> David.
> ______________________________________________________________________ 
> __
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
> ++++
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kay-Eberhard Gottschalk
Applied Physics and Center for Nano Sciences
Ludwig-Maximilians University
Amalienstr. 54
80799 Munich, Germany

Phone: +49-89-2180 3436