From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Oct 27 2003 - 13:40:51 CST
On Wed, 15 Oct 2003, Ioana Cozmuta wrote:
> 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)?
Yes. Just specify "cellBasisVector1 0. 0. $zlength" but not the others.
(More typically people want x and y periodic but not z.)
> 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?
If you want to do cylindrical boundary conditions for a system that is
periodic along the z axis (i.e., without the end caps of the cylinder) you
can just make cylindricalBCl1 and cylindricalBCl2 absurdly large (1.0e100
for example) and everything should work. To cap the ends of a simulation
that is periodic in x and y only you can take the same approach and make
cylindricalBCr1 and cylindricalBCr2 absurdly large.
NAMD doesn't provide any efficient full electrostatics for non-periodic
systems. If simple cutoff electrostatics aren't sufficient for your
system I would suggest using a periodic cell that is significantly larger
(maybe 20A) than your system in the x and y dimensions, possibly in
combination with cylindrical boundary conditions. Make sure that
cellOrigin is on the axis of the cylinder, though, or the cylinder may end
up interacting with other periodic images of your atoms.
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