dear all,
I was wondering whether there is a way to unbox the co-ordinate values for my data as this produces strange results when I attempt to plot my data... In vmd, box periodicity is somehow taken into account, but gnuplot for instance does not do this automatically, which results in halved polymer structures and other unrealistic situations as well as problems with data analysis?
Thanks in advance!
dear all,
I was wondering whether there is a way to unbox the co-ordinate values
for my data as this produces strange results when I attempt to plot my
data... In vmd, box periodicity is somehow taken into account, but
gnuplot for instance does not do this automatically, which results in
sorry, but how should a program like gnuplot know anything
about what your data represents? that is a strange way to look
at analyzing data.
halved polymer structures and other unrealistic situations as well as
problems with data analysis?
that mostly sounds, like you have to be a little bit smarter about
how to post process your data.
you can unwrap coordinates, either from within lammps through
dump_modify, or in post-processing.
please keep in mind, that most of these things are _very_ problem
specific and thus there is no good reason to automate them in
any way other than by having users build their custom postprocessing
scripts using tools like Pizza.py or VMD (cf. pbctools plugin)
to tailor the data exactly as needed for the specific purpose.
cheers,
axel.