[gmx-users] Instalation of GROMACS

[Oliver Beckstein]

Hi Tanos,

> 	I'm facing a problem to install GROMACS with double precision in my
> machine. 
> I don't know how to proceed to fix the GROMACS path in my Shell.
> I've looked for that in manuals but didn't find yet. The Shell my machine
> uses is "bash". How do I do to fix GROMACS PATH in it ?

looks like two different things to me: double precision mdrun and the
path.

Setting the path is simple:
Source the GMXRC script and you are set. For me, this means

bash$ . /usr/local/gmx314/i686-pc-linux-gnu/bin/GMXRC

(but your gromacs binaries and scripts, including GMXRC might have
been installed somewhere else). Conventionally, the double precision
mdrun binary is called 'mdrun_d' (so that you can use the single
precision mdrun at the same time), so now mdrun_d should be found in
your path:

bash$ which mdrun_d
/usr/local/gmx314/i686-pc-linux-gnu/bin/mdrun_d

If you want to learn how to set the path manually, just have a look at
GMXRC.bash in the same directory as GMXRC. 


If you haven't got mdrun_d first check if your mdrun is double
precision: You can see if it's a double precision binary by looking
at the output from 'mdrun -h'. If it's double precision it will say so:

bash$ mdrun -h
            ...
            :-) mdrun (double precision) (-:
            ...

note: if mdrun was compiled with lam support you need to start lam
first by saying something like
bash$ lamboot

If you don't have a double-precision version of Gromacs you have to
compile it; look through the README/INSTALL files and the list archive
to learn how to do it.


Oliver

-- 
Oliver Beckstein * oliver at bioch.ox.ac.uk
 http://indigo1.biop.ox.ac.uk/oliver/