CCL: GROMACS installation on Mac-OS

["Ibrahim M. Moustafa" <ria2/./psu.edu>]

 Sent to CCL by: "Ibrahim M. Moustafa" [ria2|a|psu.edu]
 Hi everybody,
    Thanks Rick for your advice; but actually my Xcode was recently updated!
I'm kind of figured out what was the problem which is: after
 installation and setting the variables I got an error message
 "Segmentation fault" when trying to issue any command...or
 trying the
 demo tutorial!
  It appeared that my installation was fine (even my compilation was
 alright......in fact compilation resulted in a code that is much
 faster than the provided binary for Mac-OSX).
 I found the whole path is required to issue GROMACS' command to run
 any program; although, the variable $GMXBIN is already set in my
 .cshrc file. This has solved the problem, but still I don't
 understand why I can't run the programs (e.g. pdb2gmx) by just typing
 "pdb2gmx" in the xterm rather than typing
 "$GMXBIN/pdb2gmx" to make
 it working!! I'm not sure if this is a an OS problem or GROMACS
 problem! or something obvious that I'm missing! Any advice would be
 appreciated.
   I haven't heard any comments regarding TINKER vs GROMACS as a
 modelling package! wish I can hear from someone though!
   thanks,
  Ibrahim
 At 12:22 AM 11/28/2006, you wrote:
>  Sent to CCL by: Rick Venable [venabler(_)nhlbi.nih.gov]
>  There can be issues with the gcc and g77 versions under MacOS X; in
>  particular, if you've kept up to date with OS patches, you may need to
>  download a newer version of the Xcode tools from the Apple Developer site.
>  I had some problems compiling CHARMM until I updated my Xcode tools.
>  --
>  Rick Venable        29/500
>  Membrane Biophysics Section
>  NIH/NHLBI Lab. of Computational Biology
>  Bethesda, MD  20892-8014   U.S.A.
>  (301) 496-1905   venabler AT nhlbi*nih*gov
>  > Sent to CCL by: "Ibrahim M. Moustafa" [ria2!=!psu.edu]
>  >
>  >    I have a limited experience in Molecular modelling of protein
>  > structures; I'd love to expand my experience in that direction. So, I
>  > have few questions for people with more experience in the field.
>  >   I wanted to install GROMACS package on my Mac-OS 10.4 according to
>  > the instructions on the GROMACS website.
>  >   First, I installed the FFTW source as instructed in the README
>  > file. Then, I installed the GROMACS binary for the MacOS-X 10.4.
>  > However, it did not work! I tried the examples provided with the
>  > package but I got "Segmentation faults"....nothing in the output.
>  > Just a blank pages while the script is running interactively.
>  > I tried to build the package myself from the source code; but again I
>  > got the same error message when running the examples' scripts!
>  > Presumably, my installation was not successful!
>  > even running the command pdb2gmx gives that error message
>  > "Segmentation fault"!!!