Re: topology file for nanotube

From: Axel Kohlmeyer (
Date: Thu Mar 10 2011 - 08:11:13 CST

On Thu, Mar 10, 2011 at 7:41 AM, sakthi kumaran <> wrote:
> Ok. I will make my statement clear. I need to compute the the interaction
> energy(interaction dominated by 12-6 LJ potential) between the capped ends
> of  nanotubes facing each other as shown in the attachment. The interaction
> between the individual nanotubes by tersoff brenner potentials or some
> equivalent. My main theme is to find the potential energy minima of such
> interacting system.

first of all. it looks like you are posting to the wrong mailing list.
since you posted to the NAMD list, people will assume
that you want to run NAMD to do the calculations that you want
and will also assume that you are using the usual tools and
force fields that NAMD users will use (unless specified to be different).

to the best of my knowledge, there is no tersoff-brenner alike
implemented in NAMD (at least not in the publicly available one).

> From your reply I got some terms cleared and confused some. So there is no
> need for an additional topology file for nanotube generated from plugin in
> vmd.......or what ...... I am not clear about it.

you have to make clear what you mean by "topology" file. there are
two common usages of that term in MD. one refers to the topology "database"
file that has topology information for small molecules or molecule fragments
that are then assembled into a .psf file, which contains the
"simulation topology",.
if you want to call it like that (it is more often use in this sense with other
MD codes). in "NAMD-slang" the topology is the former, but it looks you refer
to the latter definition.

a tersoff-brenner potential, has only implicit bonds, so there is no need
to define bond/angle/dihedral/improper topology information.

> So when I want to have capped end of the nanotube, is it possible to obtain
> the same from nanotube builder plugin in vmd or Which method do I need to
> follow?

this feature is not available in the nanotube builder.


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

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