[gmx-developers] Gromacs workflows
hess at cbr.su.se
Thu May 12 17:38:43 CEST 2011
Within the ScalaLife European project on scalable software for life
we are working on several aspects of making scientific software, among
easier to use and run in parallel.
I have a question for the Gromacs community related to two projects
One project is allowing Gromacs workflows to run on
clusters/supercomputers using a framework
that allows a simple description of the tasks and can then send it off,
run the simulation(s)
and analysis and get your results back.
Another project is a new file format for simulation input, output and
specifying analysis tasks.
We are aiming for a joint file format with at least Gromacs and Amber
and hopefully more
There are many issues to solve here and there will probably be many
fields specific for
a particular package, but we would like to have the most commonly used
in well defined fields so information can easily be exchanged between
and analysis software.
A problem is that in our group we are doing mainly non-standard things,
we do not have a good overview of what the most common tasks and needs are.
At this (very initial) point, I would like to ask the community if there
are documented workflows.
We might be able to use there, both to set up the framework and to see
we might have to store in the new file format.
I don't know if it might be useful to start a wiki page on the file
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