[gmx-users] keep the nanotube cylindrical.

Elton Carvalho eltonfc at if.usp.br
Thu May 10 16:21:31 CEST 2012

On Sat, May 5, 2012 at 7:27 PM, Za Pour <za.pour at yahoo.com> wrote:
> Dear gmx users
> I am simulation a system including carbon nanotube+water.I have done these
> things:
> However as I looked into the nvt.gro I realized that the cylindrical shape
> of carbon nanotube
>  has been changed.I am not sure what I have done is correct or not?and how
> to keep nanotube cylindrical ? any help would be really appreciated.
>       Best regards

I had a similar issue, but I modeled the CNT carbon atoms as opls_147,
trying not to change the parameters too much, so I kept the bond
lengths, angles and force constants untouched.

I noticed that removing the  [ dihedrals ] section from the resulting
topology significantly reduced the tube deformation. Since g_x2top
doesn't generate impropers and a CNT has no rotable bonds, these
dihedrals are spurious, anyway.

Also, do your tubes have open ends? If you can afford to have periodic
tubes, so that the box z length is a multiple of the tube unit cell
and the tube ends are bonded through the box wall, it seems much more
Or you could try capped tubes.

Elton Carvalho
Tel.: +55 11 3091-6985/6922
Dept Física dos Materiais e Mecânica
Instituto de Física
Universidade de São Paulo
P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil

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