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:
http://oldwiki.gromacs.org/index.php/Installation#Getting_access_to_GROMACS_after_installation
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.
Mark
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