Keep PBC box size in Z-direction constant?

From: Bjoern Olausson (
Date: Mon Feb 20 2012 - 06:37:05 CST

Hi NAMD users,

is it possible to keep the PBC-Box size in the Z-direction fixed?

I am asking because I want to run a NPT simulation in which the box
size is not allowed to shrink/extend along the Z-axis.
I tried to disable useFlexibleCell but after a few nanoseconds the
simulation crashes with the message "FATAL ERROR: Periodic cell has
become too small for original patch grid! ..."

To work around this I decreased the number of steps after which I
restart the simulation from a checkpoint to 5000ps and increased the
margin. But nothing helps. After 1.5ns the simulation just keeps
crashing no matter how small I set the individual run or how large I
choose the margin.

So is there a way to allow fluctuations along X any Y and keep Z rigid
or any other workaround to prevent the above error?


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