[gmx-users] Non-periodicity in only one direction

Rui Qiao ruiqiao at ews.uiuc.edu
Mon Dec 31 18:10:59 CET 2001

Hi, everyone:
	I am doing simulation of flow in a nano-channel right now. Becuase
the flow is confined in channel, the periodicity in one direction (let it
to be z). Because of the nature of simulaiton, electrostatic interaction
is needed.
	Someone has suggested using proper cut-off as a workaround, but
after I tried, it seems to me that the cut-off for the electrostatic is
not enough to recover the physics, i.e. I must use full electrostatics to
get reasonable results.
	Right now, I use a huge simulation box with 6 times channel width
in z direction to remove the periodicity. However, it is very inefficient,
and it is unlikely that I can afford it later. So I think I need to do
something about the code to work this out. Thus two questions:
	1. What algorithm should I use. For the PPPM, there exists some
algorithm but since PPPM is not recommended in pressure coupling, this is
not an option. For the PME, I am not sure if there exists some algorithm.
	2. Which code should I revise. 

	Thanks a lot for your time.

	happy new year.


Rui Qiao
Research Assistant
Beckman Institute, UIUC

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