<div dir='auto'>Hi,<div dir="auto"><br></div><div dir="auto">I can add that the latest versions of GROMACS never write trr frames with all nstx/v/fout options set to zero. But many years ago we always wrote a frame at mdrun termination. My memory is not that good that I recall at which version we removed this "feature", but is seems like 5.0 is affected by this.</div><div dir="auto"><br></div><div dir="auto">Cheers,</div><div dir="auto"><br></div><div dir="auto">Berk</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Oct 9, 2019 08:15, Erik Lindahl <erik.lindahl@gmail.com> wrote:<br type="attribution" /><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Hi Joseph,</p>
<p dir="ltr">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.</p>
<p dir="ltr">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.</p>
<p dir="ltr">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.</p>
<p dir="ltr">Cheers,</p>
<p dir="ltr">Erik </p>
<p dir="ltr">--<br>
Erik Lindahl <erik.lindahl@scilifelab.se><br>
Professor of Biophysics<br>
Science for Life Laboratory<br>
Stockholm University & KTH<br>
Office (SciLifeLab): +46 8 524 81567<br>
Cell (Sweden): +46 73 4618050 <br>
Cell (US): 1 267 307 8746<br></p>
<p dir="ltr">> On Oct 9, 2019, at 02:33, Joseph Coffland <joseph@cauldrondevelopment.com> wrote:<br>
> <br>
> Hello,<br>
> <br>
> I'm the lead developer at Folding@home. We've recently discovered a<br>
> problem with our Gromacs folding core. We are currently using Gromacs<br>
> v5.0.4.<br>
> <br>
> The problem we are having is that each time we stop a simulation and<br>
> restart it the .trr files grow. Some machines are configured to on run<br>
> when idle. This can lead to many start and stops which results in huge<br>
> .trr files that are difficult to return to our servers. I assume Gromacs<br>
> is writing a final frame.<br>
> <br>
> Our code calls gmx_mdrun() and then gmx_set_stop_condition(2) to break out<br>
> of the simulation. We then start again from the last checkpoint using<br>
> -cpt.<br>
> <br>
> Any advice on how to avoid this extra .trr data or remove it when we restart?<br>
> <br>
> Thanks,<br>
> <br>
> Joseph<br>
> <br>
> -- <br>
> Cauldron Development LLC<br>
> http://www.cauldrondevelopment.com/<br>
> Cell: 208-409-9128<br>
> <br>
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</blockquote></div><br></div>