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Becksteinlab / GromacsWrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).
https://gromacswrapper.readthedocs.org
GNU General Public License v3.0
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Working with Gromacs 4.x #54

Closed orbeckst closed 8 years ago

orbeckst commented 8 years ago

The default configuration file assumes Gromacs 5.x (see PR #53). If you want to use Gromacs 4.x you need a different config file such as the previous version of gromacswrapper.cfg.

With #49 we should get a mechanism to easily switch between versions.

orbeckst commented 8 years ago

I added a 4.6.5 cfg file as gromacs/templates/gromacswrapper_465.cfg in c694d5c1151a0ffbb5a0ec6f506d0299ce948524.

orbeckst commented 8 years ago

If you want to quickly "install" the gromacswrapper_465.cfg as ~/.gromacswrapper.cfg use

curl https://raw.githubusercontent.com/Becksteinlab/GromacsWrapper/develop/gromacs/templates/gromacswrapper_465.cfg -o ~/.gromacswrapper.cfg

(Note: overwrites any existing ~/.gromacswrapper.cfg file!)

pslacerda commented 8 years ago

If we put everything at config module inside functions can we just reload calling, lets say, load_setup('~/.alternative_configuration.cfg')?

orbeckst commented 8 years ago

That would be useful.

orbeckst commented 8 years ago

Note that with #68 solved you can just leave the whole [gromacs] section empty and load whichever Gromacs you like into your environment. GW will pick up all the standard tools.

orbeckst commented 8 years ago

Moving to a later milestone because the simplest solution is to not put any specific gromacs information into the cfg file and just source the Gromacs environment that you want manually and then let autoloading do its magic.

orbeckst commented 8 years ago

@pslacerda – autoloading works so well, maybe instead of reloading the whole config file we could clean the environment of GW (new purge_environment() function?) and then reload via the GMX file mechanism. (This probably mostly works already even without purging because envvars will just be overwritten. But I haven't tested it.)

In 0.6.x we are also honoring the release (although that is not working with Gromacs 2016 #96) and use it to try Gromacs 5 or 4.

Originally, this issue aimed at a making different subsections in the config file where users could define different sets of commands to go with a release. But I think for all practical cases, autoloading from the ennvironment can do this.

It might be convenient to be able to select between different GMXRC files but if this is desired then I would have another issue opened.

I think as far as supporting Gromacs 5 and 4 goes, we now do this reasonably well and I close the issue. Feel free to re-open if you feel strongly about it.