Nanopore simulation

From: subhasish chatterjee (subhas1012_at_gmail.com)
Date: Tue Feb 20 2007 - 21:58:54 CST

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.

Thank you,
Subhasish

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