From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Mar 10 2011 - 04:38:27 CST
On Thu, Mar 10, 2011 at 1:57 AM, sakthi kumaran <persakthi_at_gmail.com> 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.
axel.
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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