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

[Jennifer Rendell]

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

*******************************************************************************

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

*******************************************************************************