[gmx-users] installation

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jun 2 16:42:15 CEST 2009

Nuno Azoia wrote:
> Hello!
> Just like Manik Mayur suggested, the problem should be the links:

Making links may fix the problem of finding executables if that link 
location is already in your path, but it won't fix your other 
environment variables, or perhaps if you used configure --prefix.

> Gromacs gives you the possibility to create links to /usr/bin directory
> (ot something similar). If you didn't do that, one of the option is
> trying to run the programs using the full path. Instead of using
> pdb2gmx, try to use /usr/local/gromacs/bin/pdb2gmx. Replace
> "/usr/local/gromacs" with the directory where you install gromacs. If
> you didn't choose anything it probably is /usr/local/gromacs.

Call "source /path/to/GMXRC", then go do science.


> I hope this can help
> Nuno Azoia
> On Tue, 2009-06-02 at 12:21 +0530, Samik Bhattacharya wrote:
>> hi,I
>> i am facing a lot of troubles in installing Gromacs in my Redhat
>> machine..I've followed all the instructions given in the manual as
>> well as in the website. ialso have installed fftw,its compiling with
>> no problem. . but whenever i run pdb2gmx or command lke that its
>> giving an error "command not found". a little help regarding this
>> matter will be very encouraging. 
>> thankx
>>  Shamik
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