From: subhasish chatterjee (
Date: Wed Feb 21 2007 - 22:58:18 CST

Hi Axel,
Thank you so much for your advice.

On Feb 21, 2007, at 1:06 PM, Axel Kohlmeyer wrote:

> 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.
> cheers,
> axel.
> SC> Thank you,
> SC> Subhasish
> SC>
> SC> On Feb 20, 2007, at 11:14 PM, Mark Abraham wrote:
> SC>
> 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
> SC>
> --
> ======================================================================
> =
> Axel Kohlmeyer http://
> 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.