[gmx-users] carbon nanotube - ifnite in length ?

Dr. Vitaly Chaban vvchaban at gmail.com
Thu Sep 26 15:18:02 CEST 2013

I think this is in topology, not in MDP. With PBC, you just specify
what happens to the particle after it crosses the edge of the box in
certain direction.

I have no preference regarding LINCS vs harmonic bonds.

You can also "freeze" only the rim atoms of the nanotube from both
ends and this will be almost the same as infinite tube. This solution
is faster on my taste.

Dr. Vitaly V. Chaban

On Thu, Sep 26, 2013 at 2:39 PM, Steven Neumann <s.neumann08 at gmail.com> wrote:
> Dear Gmx Users,
> I have my carbon nanotube and I wish to make it infinite in lenght. Which
> mdp options whall be used? pbc = xy and z is the infinite dimension?
> another issue: Would you apply bonds between carbon atoms within the
> nanotube or constraints using LINCS? Which of them is less computationally
> expensive for the run?
> Thank you in advance,
> Steven
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