[gmx-users] Nanotube and Periodic Boundary Conditions

Bob Johnson robertjo at physics.upenn.edu
Sat Aug 13 02:49:48 CEST 2005

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.
Bob Johnson

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