[gmx-developers] Gromacs workflows

Berk Hess hess at cbr.su.se
Thu May 12 17:38:43 CEST 2011


Within the ScalaLife European project on scalable software for life 
sciences (www.scalalife.eu),
we are working on several aspects of making scientific software, among 
which Gromacs,
easier to use and run in parallel.
I have a question for the Gromacs community related to two projects 
within ScalaLife.
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 
different simulation
and analysis software.

A problem is that in our group we are doing mainly non-standard things, 
and therefore
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 
what information
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 
format requirements.


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