CCL: GROMACS installation on Mac-OS
- From: "Ibrahim M. Moustafa" <ria2/./psu.edu>
- Subject: CCL: GROMACS installation on Mac-OS
- Date: Wed, 29 Nov 2006 17:15:38 -0500
Sent to CCL by: "Ibrahim M. Moustafa" [ria2|a|psu.edu]
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
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
I haven't heard any comments regarding TINKER vs GROMACS as a
modelling package! wish I can hear from someone though!
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download a newer version of the Xcode tools from the Apple Developer site.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"!!!