Dear Amber users !
I am using cpptraj for some basic post-processing of production run
trajectory with the aim to reduce PBC effects for visual inspection
cpptraj.mpi -p complex.prmtop -y production.nc -x production_nopbc.nc
-i cpptraj.in
where the cpptraj.in consists of only the autoimage command.
Basically it works OK but I am stuck on the task when I need to save
each 5th snapshot to reduce the size of the output file.
For this aim I modified my cpptraj script explicitly adding
trajout production_nopbc.nc netcdf offset 5
and running cpptraj without -x as
cpptraj.mpi -p complex.prmtop -y production.nc -i cpptraj.in
which always produces an error either
"file production_nopbc.n already in use"
or cpptraj.mpi could not handle trajout in parallel.
Since the first version (with -x) works very well in parallel, are
there any trick to specify offset outside of the cpptraj.in script ??
Many thanks in advance
Enrico
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Received on Wed Aug 30 2023 - 04:00:02 PDT
