blank between nanotube and the bulk water

From: fereshteh moradi (f78moradi_at_gmail.com)
Date: Fri May 07 2010 - 23:29:22 CDT

Hello

I have simulated the flow of water through a bundle of four nanotubes for
about 20 ns. The config file was prepared as namd tutorial, however, it was
unexpected to see a large distant blank (about 2 nm) between exiting water
molecules from nanotube and the down-stream bulk fluid. I have tried to
change pbc dimensions but it didn't have any effect.
Please help me with some applicable hints, maybe I have forgotten some
keypoints.

Regards

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