Re: Nanopore simulation

From: Mark Abraham (
Date: Tue Feb 20 2007 - 22:14:46 CST

subhasish chatterjee wrote:
> Dear All,
> I am trying to perform molecular dynamics simulation of nanotube
> /nanopore. I was wondering whether it is possible to utilize the VMD
> program to generate the structure of nanotube/ nanopore and all other
> necessary parameter files for use in MD simulations.
> I saw the NAMD tutorial of the water transport through nanotube, but I
> did not find any clear information about the preparation of structural
> files (pdb/psf or Amber parameter files) of nanotube/nanopore. I would
> also like to study the voltage driven translocation of bio-molecules
> through nanopore. I would appreciate any suggestion regarding the use
> of VMD and NAMD in the MD simulations of nanopores.

I infer from your questions that some good advice for you would be to
learn to walk well, before you try to run. I suggest you start with all
of the tutorial material available on the VMD and NAMD websites. Then
consider attending one of the workshops that is held for learning their
proper use. Attempting to do any of the above procedures too early is a
recipe for frustration and wasted computer time.


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