AMBER Archive (2009)

Subject: [AMBER] how to use two dimensions periodic boundary ?

From: Nancy (
Date: Wed May 20 2009 - 20:32:50 CDT

Dear all,
  I put a layer of water in the nozzle of carbon nanotube,because of three dimensions periodic boundary , water molecules enter carbon nanotube ,and they come out,then they re-enter the initial nozzle.In deed,I don't want such result , can i use two dimensions periodic boundary condition which are in X and Y directions, not Z derection to keep water from re-entering the initial nozzle,if so ,how should i do? can anybody give me some advice ? Thanks in advance.

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