[gmx-users] upgrade version - "make distclean"?

[Mark Abraham]

Low Soo Mei wrote:
> Hi,
> 
> I would like to upgrade from version 3.3.2 to 3.3.3 on my local 
> computer, non-parallel for both.  Can I confirm that I should
> 
> 1)  cd to the gromacs-3.3.2 directory
> 2) type "make distclean"
> 3) then delete the entire gromacs-3.3.2 directory
> 
> , to clean 3.3.2 off my computer entirely?

2) is optional, since 3) does everything it will do. Usually, "make 
uninstall" is the way to uninstall, but I haven't done it and don't know 
how thorough GROMACS is here. "make distclean" is only useful to clean 
up the sources when you're tinkering with the source code and want to 
ensure things are in sync.

> I am still optimizing my MD simulations and would like to attribute 
> simulation errors to only my simulation parameters and not to some 
> installation/upgrade problem.  No previous advice on upgrading was 
> available from Google or the Gromacs wiki or mailing lists.

It happens so rarely that it's not a big deal :-)

One thing you can do is to install a GROMACS version into a particular 
directory, like /usr/local/gromacs-3.3.3 with the --prefix option to 
configure (see configure --help) and then everything is contained within 
that directory (unless you use "make links"). You source 
/usr/local/gromacs-3.3.3/bin/GMXRC from your shell init script and go on 
with life. Later when you come to upgrade, delete 
/usr/local/gromacs-3.3.3 if it makes you happier, but you really can 
leave it around in case you need it. Then you install GROMACS 4.0 into 
/usr/local/gromacs-4.0 as before, and change to sourcing the new GMXRC.

Mark