From: Axel Kohlmeyer (
Date: Wed Feb 21 2007 - 12:06:08 CST

On Wed, 21 Feb 2007, subhasish chatterjee wrote:

SC> Hi Mark,
SC> Thanks for your reply. Any suggestion for the preparation of
SC> nanotube/nanopore structural and parameter files would be very
SC> helpful.
SC> There is very effective information regarding the use of VMD and
SC> NAMD in biomolecular MD simulation in the tutorial materials and
SC> website, and thus it is going fine so far.
SC> A little more elaborate description of the nanopore simulation would
SC> be very beneficial.

well, mark's point is, that if you were more comfortable with using
the available tools already, you wouln't even ask a question this
generic. if setting up a simulation like you have in mind, would
be that common, so it justifies the effort of writing a tutorial
about it, you wouldn't have a research project (since others would
have done it before). hence, the one and only advice and help you
can get, is to practice on simpler examples until you are deservedly
confident in using them.

now to generate coordinates for a single walled carbon nanotube
(i don't know what you mean by 'the' nanopore, i guess this is the
same). you just go into the literature. there are a few simple
expressions on how to compute the coordinates (you have to make
a choice what kind of an (m,n)-nanotube you want to produce), and
there are also some parameter sets that you can use. there also
are many open questions in your request (how should your total
system look like? do you want to embed the nanotube into something?
what else should be in your system? etc. etc.). if you want specific
help, you have to provide more specific information.

furthermore, since you were writing about voltage driven transport,
you should have a very close look to non-equilibrium MD. this is
a wholly new can of worms and can be a lot of trouble in itself.
be prepared to need very large quantities of compute power at
your disposal.


SC> Thank you,
SC> Subhasish
SC> On Feb 20, 2007, at 11:14 PM, Mark Abraham wrote:
SC> > subhasish chatterjee wrote:
SC> >> Dear All,
SC> >> I am trying to perform molecular dynamics simulation of nanotube /
SC> >> nanopore. I was wondering whether it is possible to utilize the
SC> >> VMD program to generate the structure of nanotube/ nanopore and
SC> >> all other necessary parameter files for use in MD simulations.
SC> >> I saw the NAMD tutorial of the water transport through nanotube,
SC> >> but I did not find any clear information about the preparation of
SC> >> structural files (pdb/psf or Amber parameter files) of nanotube/
SC> >> nanopore. I would also like to study the voltage driven
SC> >> translocation of bio-molecules through nanopore. I would
SC> >> appreciate any suggestion regarding the use of VMD and NAMD in the
SC> >> MD simulations of nanopores.
SC> >
SC> > I infer from your questions that some good advice for you would be
SC> > to learn to walk well, before you try to run. I suggest you start
SC> > with all of the tutorial material available on the VMD and NAMD
SC> > websites. Then consider attending one of the workshops that is held
SC> > for learning their proper use. Attempting to do any of the above
SC> > procedures too early is a recipe for frustration and wasted
SC> > computer time.
SC> >
SC> > Mark

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.