[gmx-users] Incomplete frame,while running trjconv .....
Mark.Abraham at anu.edu.au
Tue Jan 5 22:53:46 CET 2010
pavan payghan wrote:
> 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?
A complete frame was not written to the trajectory file on disk, but it
was fine in the program's memory, and so the run continued. The magic in
modern buffered I/O means there is no warrant issued by the system that
instructions to write to disk will be honoured or the program exit.
> what else reason may be behind this and wht are the possible ways
> to overcome this problem?
Get more disk. Plan your usage better. See
> 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?
We generally try to model a physical system, and either validate a
methodology against experimental data, or re-use a validated protocol.
In either case, an NVT or NPT or other ensemble might be indicated, but
it depends on what you're doing.
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