[gmx-users] Does mdrun know when other gromacs programs move its destination .xtc?

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 13 18:13:22 CEST 2006

chris.neale at utoronto.ca wrote:
> When an output .xtc destination of mdrun is backed up while the original version
> of mdrun is still running, does mdrun know and does the output get handled
> correctly?

No, but it works the way you'd want it to.

> So two versions of mdrun are running simultaneously in the same directly
> (identified by the original log file which continues to show additional md
> steps). The strange thing is that #traj.xtc.2# continues to be updated and is
> now the size that I expect it to be as if it is getting properly updated.
> Is this possible? Does mdrun know when "Back Off!" occurs and redirect its
> output appropriately?

Filenames are just indexes into lists of the locations where chunks of 
files are stored. On a typical file system, you can change the name 
without changing the underlying structure - just like a real file in a 
filing cabinet. Once mdrun has opened the file (the backup procedure 
happens before that, once only) it keeps it open, referring to the 
underlying structure and not using the name again. Hence, renaming it is 
irrelevant. You can test this yourself by renaming it mid-output some 
time. An additional test of the integrity of your file is to work out 
the simulation time that you introduced the potential discontinuity, and 
looking to see what happens at that point of the trajectory.


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