From: Pavan G (pavan.namd_at_gmail.com)
Date: Wed Mar 27 2013 - 12:51:25 CDT
Hello All,
I am trying to run a simulation with 3 components; water, porous media and
vapor. Without the vapor region the box dimensions are;
cellOrigin 36.914 50.465 10.028
cellBasisVector1 98.480 0.000 0.000
cellBasisVector2 0.000 81.957 0.000
cellBasisVector3 0.000 0.000 83.311
I want to add a 20A vapor region on the +z side of the porous media. This
obviously means that the simulation has to be 2d periodic (in x and y). To
achieve this I removed the 'cellBasisVector3' line and since the vapor
region adds 20A in the z dimension, the center of the box will shift by 10A
along z. So I now have
cellOrigin 36.914 50.465 20.028
cellBasisVector1 98.480 0.000 0.000
cellBasisVector2 0.000 81.957 0.000
# cellBasisVector3 0.000 0.000 83.311
I had to remove PME since a sample run failed complaining that PME requires
PBC in all 3 directions (or something on those lines).
So when I ran this simulation w/o PME and w/o z axis PBC, I got few ps of
data before it died with this error:
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.
I did restart from the last checkpoint and it ran for few more ps and dies
with the same error. useFlexibleCell is already set to 'no'.
>From the forums I found that increasing the 'margin' in the config file
helps. I increased this from default to 1.5. The simulation is running fine
and looks fine as well.
I am writing to check if my approach is correct. Is this how you would do
it?
Thank you
PG
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