[gmx-users] Carbon Nanotube and Periodic Boundary Conditions

David van der Spoel spoel at xray.bmc.uu.se
Fri Jul 22 08:59:08 CEST 2005

On Thu, 2005-07-21 at 17:39 -0400, Bob Johnson wrote:
> Hello,
> I am currently building a system that contains carbon nanotubes and single
> stranded DNA. I am studying the interactions between them. I would like to
> create an array of infinitely long nanotubes using 3D periodic boundary
> conditions. I'm starting out with a tube about 7.5nm long. How would I set up
> the system such that the carbons at the ends of the tube are bonded to those of
> the adjacent tube image?
generate a topology with x2top (search the list)
and use pbc=full

> Thanks,
> Bob Johnson
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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