cylindrical boundary conditions

From: Ioana Cozmuta (
Date: Wed Oct 15 2003 - 16:48:08 CDT


Is it possible to use NAMD for a system which is periodic in the z
direction but not in the x and y directions? Like a cylinder of infinite
z length (when the cylinder axis is aligned with the OZ axis)?

To my understanding the cylindrical boundary conditions are non-periodic
and use harmonic potentials to prevent molecules from "flying away". What
method is best to use to calculate electrostatic interactions when chosing
cylindrical BC?

Any advice would be appreciated. Thanks,

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