[gmx-users] Can 3.3.3 and 4.0.5 version exist at the same time?

Mark Abraham Mark.Abraham at anu.edu.au
Fri Sep 4 06:22:45 CEST 2009

Chih-Ying Lin wrote:
> Hi
> The 3.3.3 and 4.0.5 version were installed under =>
> *
> source /usr/gromacs/4.0.5/setup.sh
> source /usr/gromacs/3.3.3/setup.sh*

I've no idea what these scripts are, but the correct procedure is to 
follow the advice about GMXRC here:

Now you should be able to source the corresponding file and get 
everything correctly adjusted for a particular GROMACS version in shell 
that sourced the file.

Alternatively, you could use configure --program-suffix=_xxx and have 
both available in the same shell, potentially.

> *The 4.0.5 version is currently the default one.*
> I want to compare the computation results from 4.0.5 version and 3.3.3
> version.
> So, I write the
> *source /usr/gromacs/3.3.3/setup.sh*
> into both my .cshrc file and .pbs file.
> After this command for 3.3.3 version
> grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o
> 6LYZ-EM-vacuum.tpr
> I obtained the errors shown on the screen.
> -------------------------------------------------------
> Program grompp_mpi, VERSION 4.0.5
> Source code file: statutil.c, line: 727
> Invalid command line argument:
> -np
> -------------------------------------------------------

Clearly the first grompp_mpi in your path is still the 4.0.5 version. If 
your setup.sh merely appends the 3.3.3 path then your strategy won't 
work. IIRC, using GMXRC will take care of this issue.

Also note that there's no need to compile MPI versions of the tools - 
configure once with MPI and use "make mdrun && make install-mdrun", and 
once without MPI and "make && make install". In some circumstances, this 
approach can be essential.


More information about the gromacs.org_gmx-users mailing list