How to do "if-then " statement every time step

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My problem is that, for the translocation process, as you said,
it is pointless to get an exact translocation time for a single run,
so I need to run the simulation eg. 1000 times, each time I record the
translocation time,
then I get a histogram on that. If I do post-processing, which means I need
to store data for
1000 runs, which might take a huge space.

no it won't, if you had paid attention to what i had written earlier.

there is no need to write out the entire system. depending on the
relative sizes, you would only need to record the trajectories of a
few relevant atoms and not even at every step. and then the size issue
is not an issue at all.