[gmx-users] Why GROMACS demo fails?

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jan 16 16:35:19 CET 2007

Hi Vladimir,

It should also be in the directory which you fed to ./configure with
the option --prefix=
There, there should be a directory bin/ which contains all the
binaries. In addition, it contains a script GMXRC, which you can use
to set all the environment variables properly, including the PATH
(source GMXRC).

Besides, you may also want to try the tutorial at
http://nmr.chem.uu.nl/~tsjerk/MDCourse/ ;)

Good luck,


On 1/16/07, Vladimir Korostelev <vladimir.v.korostelev at rambler.ru> wrote:
> Thanks for help with GROMACS installation.
> I have installed GROMACS and it seems successfully because ./luck has
> brought
> a quote this time (gcq#119 "Bring Out of Gimp" (Pulp Fiction))!
> However my attempt to run demo in /tutor subdirectory has failed - a
> window popped
> up with a message 'pdb2gmx: command not found'.
> pdb2gmx binary program is in /home/vladimir/gromacs-3.3.1/src/kernel
> How I can make it visible for other places so that demo would work?
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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