Hello, everybody:
I’m working with a colleague who has some scripts that are designed to analyze data from Gromacs simulations with trajectory files in xtc format. We’re running LAMMPS simulations, but the requirements of the xtc format seem to suggest that the run has to be completed for the xtc file to be written; because of the job time limitations on the machines we’re running on, this really isn’t possible.
The other idea we have is to process existing dump files into the xtc format, but we’re wondering if there are any tools out there that would do this conversion already, or if it’s something we’d have to write ourselves. (For example, I can’t see an option for this already available in pizza.py.)
Thanks,
–AEI
Hello, everybody:
I'm working with a colleague who has some scripts that are designed to
analyze data from Gromacs simulations with trajectory files in xtc format.
We're running LAMMPS simulations, but the requirements of the xtc format
seem to suggest that the run has to be completed for the xtc file to be
written; because of the job time limitations on the machines we're running
on, this really isn't possible.
what do you mean by completed?
that the whole trajectory should be one file
or that you have let your jobs go until they get
killed by the batch system?
can you elaborate a bit more?
hmmm.... what kind of machine are you running on?
if i'd send you some code to have a signal handler
installed that would terminate the run and write a restart
and does some kind of "emergency exit". would that help.
i've done similar things for other codes and it might be
a useful feature for LAMMPS.
if it is just about xtc files being appended instead of
overwritten, then it is probably better to use a variable
in the file name and then set the variable to unique numbers
(i prefer the batch job id) and use the -var flag.
The other idea we have is to process existing dump files into the xtc
format, but we're wondering if there are any tools out there that would do
this conversion already, or if it's something we'd have to write ourselves.
(For example, I can't see an option for this already available in pizza.py.)
does it have to be .xtc?
if i remember correctly, the catdcd code from the schulten folks can
write .trr. which should be good enough for gromacs tools (and faster).
cheers,
axel.