[gmx-developers] Gromacs workflows

[Berk Hess]

On 05/12/2011 05:49 PM, Shirts, Michael (mrs5pt) wrote:
>> 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
>> information
>> in well defined fields so information can easily be exchanged between
>> different simulation
>> and analysis software.
> Interesting. I wonder if it might make more sense rather than to come up
> with a new format that other tools need to support, build tools that can
> intercovert between input/output files more easily.  Then all that needs to
> be done is to write importers/exporters, rather than having to rewrite
> codes.  This has some advantages:
>
> * Nothing breaks -- no need to worry about portability between new and older
> formats for existing code.
> * Decoupling changes in file writing/reading from changes in the main
> simulation codes.
> * If there are desires to move to a new general format eventually, it can be
> done gradually, as weak coupling between codes already exists.
> * Third parties can write importers/exporters, so having the main developers
> of each software code on board is not necessary.
>
> Incidentally, my group is working on a version of something like this right
> now; we've only got proof of principle working so far (can import and output
> from Gromacs to an abstract internal representation), but are now moving to
> supporting other codes, and parameterization schemes.  I'd be very
> interested in connecting with other people on such a project.
>
I am also not in favor of yet another file format.
But we had anyhow already decided to move to xml for several types of files
and if other MD simulation packages are also interested we might actually
be able to achieve a good and widely used format.
An issue are our trajectories, which we would not want to have in ascii.
But note that I'm not at all a file format expert.
>> 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.
> David Mobley, John Chodera, and I have a fair amount of work done on
> automatic workflows for free energy calculations.
I was thinking of more "standard" things than that, but maybe free energy
calculations belong to the standard repertoire now.

Berk
> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
>
>
>> From: Berk Hess<hess at cbr.su.se>
>> Reply-To: Discussion list for GROMACS development<gmx-developers at gromacs.org>
>> Date: Thu, 12 May 2011 11:38:43 -0400
>> To: Discussion list for GROMACS development<gmx-developers at gromacs.org>
>> Subject: [gmx-developers] Gromacs workflows
>>
>> Hi,
>>
>> 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
>> information
>> 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.
>>
>> Berk
>>
>> -- 
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