[gmx-users] Incomplete frame,while running trjconv .....

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Jan 5 19:00:34 CET 2010

Your disk was full and the .xtc file could not be completely written,  
therefore you have an incomplete frame. I think that you have answered  
your own question here. If I was you, I would trjconv -e to get the  
full trajectory minus the last incomplete frame for a good .xtc file.

There are other reasons why you could have an incomplete frame (e.g.  
NFS delay if you trjconv, gmxcheck, or otherwise access your file  
during the run) but I don't think that this case warrants any such  
esoteric explanation.

Are you suggesting that your run went so far beyond this stage that  
you no longer have a .cpt file that was created before the incomplete  
frame was written (including _prev.cpt)? In this case, I would simply  
extract a .gro from the last good frame of the .xtc and use grompp to  
restart the run. If you have the .trr and .edr frames near this point  
then you can use them for a proper restart. Reassigning velocities at  
one arbitrary point in a simulation should not be a problem though and  
I would not consider it to be a significant flaw in any simulation.


-- original message --

     i have to create .xtc file to save my disk space,but while i was running
it using trjconv i got warning message
     "incomplete frame".Actually i was running my system on four nodes with
mdrun_mpi but it stopped due to
      unavailability of disk space so from this it is certain that my system
run well and ,when i tried to run trjconv i got such error
      message ,surprisingly this incomplete frame is in the middle portion of
the simulation.
      if this frame was incomplete how come mdrun will continue the
simulation after that time frame?
      what else reason may be behind this and wht are the possible ways to
overcome this problem?
      another thing im using pressure coupling during production mdrun has it
been the reason ?
      can u also explain why we generally cut off pressure coupling during
production mdrun?
                                             will you please help me
                                                  THANKING YOU

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