pavan payghan wrote:
HI
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
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume
another thing im using pressure coupling during production mdrun
has it been the reason ?
No relevance.
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.
Mark
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