[gmx-users] problem regarding installation of gromacs-4.5.5

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 15 14:57:19 CEST 2012

On 6/15/12 8:45 AM, Nidhi Jatana wrote:
> Dear Sir/Madam
> I checked up in the system, there was one version of gromacs in /opt/bio/. I
> removed that and I reinstalled gromacs using the following commands:
> tar -xvf gromacs-4.5.5.tar.gz
>   cd gromacs-4.5.5
>    ./configure --program-suffix="_mpi"
>    make
>    make mdrun -j 8
>   make install
>     make install-mdrun
>     make links

This is not a correct installation procedure.  Please follow the instructions at:


> But now, its not running any commands. I made links and I made entry into the
> .bashrc file by putting up the following command:
> export GMXRC=/usr/local/gromacs/bin/GMXRC
> Now, I am unable to run any coomand of gromacs. What could be the possible solution.

Now you're maintaining two versions of Gromacs, which in itself is not a 
problem, as long as your environment is configured correctly, but you have to be 
careful in setting that up.  I don't have an explanation as to why no commands 
are working, but you may have to re-configure your environment to only recognize 
one Gromacs installation at a time.

If you no longer need an old version, you can simply remove it.




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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