[gmx-developers] Question about restarting

Erik Lindahl erik.lindahl at gmail.com
Wed Oct 9 08:15:31 CEST 2019

Hi Joseph,

If this happens in a released version of Gromacs that's supported (last version or two, depending on severity), it's something we'll look into if there's a redmine filed with examples of how to reproduce it. If you can't reproduce it with a normal recent Gromacs release, it should only be a matter of tracking down the differences.

In general there is NO reason to ever use full-precision TRR trajectories for any modern simulations given that we have exact restarts - it's just massive data bloat. I also hope you realize that it's a remarkably bad idea to use a 5-year-old version (and not even the latest patch of that release) that hasn't been supported for years for scientific work.

In principle we're also quite open to provide support both for old code versions, development outside the Gromacs source tree or even private versions, but that would typically involve a consulting contract.



Erik Lindahl <erik.lindahl at scilifelab.se>
Professor of Biophysics
Science for Life Laboratory
Stockholm University & KTH
Office (SciLifeLab): +46 8 524 81567
Cell (Sweden): +46 73 4618050 
Cell (US): 1 267 307 8746

> On Oct 9, 2019, at 02:33, Joseph Coffland <joseph at cauldrondevelopment.com> wrote:
> Hello,
> I'm the lead developer at Folding at home.  We've recently discovered a
> problem with our Gromacs folding core.  We are currently using Gromacs
> v5.0.4.
> The problem we are having is that each time we stop a simulation and
> restart it the .trr files grow.  Some machines are configured to on run
> when idle.  This can lead to many start and stops which results in huge
> .trr files that are difficult to return to our servers.  I assume Gromacs
> is writing a final frame.
> Our code calls gmx_mdrun() and then gmx_set_stop_condition(2) to break out
> of the simulation.  We then start again from the last checkpoint using
> -cpt.
> Any advice on how to avoid this extra .trr data or remove it when we restart?
> Thanks,
> Joseph
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> Cauldron Development LLC
> http://www.cauldrondevelopment.com/
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