Re: topology file for nanotube

From: Axel Kohlmeyer (
Date: Thu Mar 10 2011 - 04:38:27 CST

On Thu, Mar 10, 2011 at 1:57 AM, sakthi kumaran <> wrote:
> Hi
>     I am new to namd.I need to compute the free energy of a (5,5) nanotube

what kind of "free energy" do you need? i assume you are aware
that absolute energies are completely bogus in most computational
methods, only energy differences have a meaning.

you should also note, that when using a classical force field, you
make a large approximation for the nanotube itself by treating it
as a gigantic "web" of benzenes (it is not as bad, if you are only
interested in the interactions of something else with a nanotube).

people who study mechanical properties of nanotubes often use
the AIREBO manybody potential, which is a much more detailed
model, but as a manybody potential also more expensive to compute.
for electrical properties, of course, you need some form of quantum
chemical calculation...

> in vacuum.So where can I get the topology file for the same.

a topology in charmm lingo does not exist. you cannot build
nanotubes from a linear chain of residues like peptides. on the
other hand, a (carbon) nanotube has only one atom type so there
is no real need to compare to a template of internal coordinates
and bonds; this topology information can be easily inferred from
the geometry.

> I also need clarifications of the following
> 1. Whether the topology file is different for different chirality of
> nanotubes.

no. see above.

> 2. whether the topology file is different when the medium chnges say vaccum
> to water.

no. see my comments from above about the crudeness of the model.

> 3. whether the topolgy files for (5,5) and (10,10) nanotubes can be used
> together for (5,5)@(10,10) configuration.

this is irrelevant. see above.


Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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