Re: vmd-l: Re: Nanopore simulation

From: subhasish chatterjee (
Date: Tue Feb 20 2007 - 23:54:32 CST

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

On Feb 20, 2007, at 11:14 PM, Mark Abraham wrote:

> 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.
> Mark

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