[gmx-users] Help after gromacs installation

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 29 17:33:16 CEST 2008

Quoting fabracht sdf <fabracht at gmail.com>:

> Hello friends from user's list. First of all, thank you very much for all
> the help with my previous problems. They allowed me to finally install
> gromacs with mpi support. But now I have another problem.
> After the installation I tryed to run the test and it failed all the way.
> Then, when I typed grompp, or mdrun, or any other gromacs's command, i get
> the following line
> "bracht at linux-k22j:~/Desktop/gromacs-3.3.2> grompp
> bash: grompp: command not found"
> The installation process told me:
> "GROMACS is installed under /usr/local/gromacs."
> And i checked, it is actually there. So, maybe I should do something extra
> in order to use gromacs, but honestly i haven't got a clue on what to do. I
> tryed to search on the archives but it seems that no one has ever had a
> problem like this.

By default, your Linux system will look for executables in pre-defined PATHs
(/usr/bin, /usr/local/bin, etc), so you need to tell your computer where to
find your Gromacs installation.  To see where your computer is searching for
executables, try 'echo $PATH'

You would have to specify a PATH for Gromacs in your .bashrc file like:


Then try 'which grompp'


> Thank you in advance
> Fabrício Bracht


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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