[gmx-users] Operation of tutorial

Oliver Beckstein oliver at biop.ox.ac.uk
Fri Dec 3 22:59:55 CET 2004

Hi Joe,

I am not using MacOS myself but perhaps it's more a simple
shell/environment problem.

> I am now working through the tutorials and have hit a second snag, in that
> my computer is not recognizing the commands ³demo² or ³pdb2gmx². I have
> successfully configured and installed both fftw and gromacs.  Upon
> installation, the program placed the /bin file (which contains pdb2gmx)
> inside of another directory, powerpc-apple-darwin7.6.0. I tried setting the
> path in two ways using the setenv command described in the online
> documentation, first as (in my case) /Users/jbozell/gromacs/bin, and then as
> /Users/jbozell/gromacs/ powerpc-apple-darwin7.6.0/bin.  In both cases, when

If you installed gromacs with the canonical 'make install' then you should
also have a file .../gromacs/powerpc-apple-darwin7.6.0/bin/GMXRC
Then you should be able to setup the Gromacs environment by sourcing it,

  source .../gromacs/powerpc-apple-darwin7.6.0/bin/GMXRC

(where ... = ~ or /Users/jbozell or whereever you installed it). This
should also set paths to libraries, eg check with 'echo $GMXDATA'. In
particular, it adds the bin directory to your PATH. You should now be able
to execute all gmx programs; check with

  pdb2gmx -h

For problems with demo I'm just guessing that perhaps the current
directory '.' is not in your PATH and then you'd need to execute './demo'
instead of 'demo'. 

> I moved to the directory containing the first demo, entering ³demo² resulted
> in the reply ³command not found².  I have also copied the bin file from its
> initial location into the gromacs file and reset the path as
> /Users/jbozell/gromacs/bin.  Again, the command is not recognized. I get the
> same result from entering pdb2gmx.

(I my comments above I assumed that the directoryt layout is the one
after the initial installation.) Btw, you can have a look at GMXRC and
GMXRC.csh (and the others) to find out where the Gromacs installation
procedure beliefs your files to be located. 


Oliver Beckstein * oliver at biop.ox.ac.uk

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