[gmx-users] Nanotube and Periodic Boundary Conditions

David spoel at xray.bmc.uu.se
Sat Aug 13 08:22:56 CEST 2005

On Fri, 2005-08-12 at 20:49 -0400, Bob Johnson wrote:
> Hello everyone,
> I am simulating an infinate carbon nanotube and a single stranded DNA molecule.
> I am using the Amber force field for the DNA molecule. Thus, I generate my
> topology and coordinates in Amber's Xleap and then convert the topology to the
> GROMACS format. However, it seems that I am unable to use periodic boundary
> conditions for the nanotube this way. I was told before that I should generate
> the nanotube topology using x2top and use pbc = full. Can I still have an
> infinite nanotube when the topology is generated with another program? I always
> use pbc = full and it seems that it isn't working if I don't use x2top.

These things are unrelated. If you want to use constraints you have to
download the CVS version of GROMACS.

Yuo will have to merge the topologies by hand using suitable AMBER
replacements for the atomtypes in the nanotube.

> 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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