From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Wed Mar 09 2016 - 21:23:05 CST
I would like to apply periodic boundary conditions only in X and Y
directions. In my config file I used the following entry:
# Periodic Boundary Conditions
cellBasisVector1 70.0 0. 0.0
cellBasisVector2 0.0 70.0 0.0
cellBasisVector3 0.0 0 0.0
cellOrigin 30.0 30.0 32.5
When I submit the job it runs for a while until I see the following error:
WRITING COORDINATES TO DCD FILE ar_force_out.dcd AT STEP 20750
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
How can I address this error? Is this the right way to set up PBC in 2
My simulation cell is actually around (~61 ~61 ~62), as measured by
minmax. I played with numbers and noticed that my simulation runs
longer if I increase both the margin and cell basis vectors.
I saw some of the older threads in the archives where the margin was
discussed but it's not clear how large should it be. If I want to run
my simulation for 500 000 steps, what margin should I set up?
Also, when choosing cell basis vector, how much bigger should it be
than what is measured by "measure minmax"?
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